Package {RDML7}

RDML7: qPCR data import, conversion, validation, and export

Description

'RDML7' provides S7 classes and a functional API for Real-time PCR Data Markup Language (RDML) data and several instrument/vendor formats. The canonical API uses lower camel case and value semantics: functions that modify an object return a new 'rdmlType' that should be assigned back.

Main workflow

A typical workflow is:

1. Read a file with 'readRDML()'. 2. Inspect it with 'summary()' and 'validateRDML()'. 3. Build a metadata table with 'asTable()'. 4. Extract curves with 'getFData()'. 5. Modify or add curves with 'setFData()'. 6. Export with 'writeRDML()'.

Use 'listRDMLFormats()' to list registered file formats and their capabilities.

Value semantics

RDML objects are S7 value objects, not mutable R6 environments. Therefore:

“' rdml <- setFData(rdml, fdata, description) “'

rather than relying on in-place reference mutation.

File-format registry

Built-in readers cover RDML/XML and several vendor/table formats. The registry is extensible through 'registerRDMLFormat()' and 'loadRDMLModule()'. Third-party importers may return either an 'rdmlType' directly or an 'rdmlImportData' intermediate representation.

RDES

RDES (Real-time PCR Data Essential Spreadsheet Format) is supported for import and export. It is a UTF-8, tab-separated format for one run, with amplification and melting data stored in separate files. See 'vignette("RDES", package = "RDML")'.

Legacy API

Historical names such as 'AsTable()', 'GetFData()', 'SetFData()' and 'MergeRDMLs()' remain available as compatibility wrappers. New code should use the camelCase API.

Author(s)

Maintainer: Konstantin A. Blagodatskikh k.blag@yandex.ru

Authors:

• Konstantin A. Blagodatskikh k.blag@yandex.ru

Other contributors:

• Stefan Roediger stefan.roediger@b-tu.de [contributor]

• Michal Burdukiewicz michalburdukiewicz@gmail.com [contributor]

• Andrej-Nikolai Spiess a.spiess@uke.de [contributor]

See Also

'readRDML()', 'writeRDML()', 'asTable()', 'getFData()', 'setFData()', 'validateRDML()', 'summary()', 'listRDMLFormats()'

annotationType S7 class

Description

Free-form property/value annotation attached to a sample. Inherits from 'rdmlBaseType'.

Usage

annotationType(property = NA_character_, value = NA_character_)

Arguments

Format

An S7 class.

Value

An S7 object of class 'annotationType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'property'

'character(1)' or 'NA'. Annotation property name.

'value'

'character(1)' or 'NA'. Annotation value.

See Also

'sampleType'

Represent RDML structure as a dendrogram

Description

Groups stored data hierarchically by experiment, run, target, sample type, and curve type ('adp' or 'mdp'). Leaf labels contain the number of matching reactions.

Usage

asDendrogram(x, ...)

Arguments

Value

A base R 'dendrogram' object. An empty RDML object returns an empty dendrogram; plotting it produces a warning.

Arguments for the 'rdmlType' method

'plotDendrogram'

Logical. Plot the dendrogram immediately? Defaults to 'TRUE'. Use 'FALSE' to build the object without opening a graphics device.

See Also

'summary()'

Examples

rdmlFile <- system.file(
  "extdata", "BioRad_qPCR_melt.rdml", package = "RDML7"
)
rdml <- readRDML(rdmlFile, showProgress = FALSE)
tree <- asDendrogram(rdml, plotDendrogram = FALSE)
tree

Build a metadata table from an RDML object

Description

Creates one metadata row for every target-specific 'dataType' stored in an RDML object. This table can be inspected directly or supplied as 'request' to [getFData()].

Usage

asTable(x, ...)

Arguments

Value

A keyed [data.table::data.table] with 'fdataName' followed by the selected built-in and custom columns. Positions use canonical plate labels such as 'A01'.

Arguments for the 'rdmlType' method

'columns'

Character vector selecting built-in columns, or 'NULL' for all built-in columns. Available values are 'expId', 'runId', 'reactId', 'position', 'sample', 'target', 'targetDyeId', 'sampleType', 'adp', and 'mdp'.

'namePattern'

Character template or expression used to create the unique 'fdataName' for each curve. Character templates use '{field}' placeholders, for example '"{position}_{target}"'.

'includeHidden'

Logical. Include experiments whose identifiers start with '.'? Defaults to 'FALSE'.

'treatNullAsNa'

Logical. Convert 'NULL' results from custom expressions to 'NA'? Defaults to 'FALSE'.

'default', 'addColumns'

Deprecated compatibility arguments for named lists of base and additional expressions. New code should use 'columns' and named expressions in '...'.

Custom columns

Expressions in '...' can use the scalar values 'expId', 'runId', 'reactId', 'position', 'sample', 'target', 'targetDyeId', 'sampleType', 'adp', and 'mdp'. They can also inspect the current 'experiment', 'run', 'react', and 'data' objects and the top-level 'samples', 'targets', 'dateMade', 'dateUpdated', 'id', 'experimenter', 'documentation', 'dye', and 'thermalCyclingConditions' collections.

Named custom columns may be referenced by 'namePattern' placeholders.

See Also

'getFData()', 'setFData()'

Examples

rdmlFile <- system.file("extdata", "lc96_bACTXY.rdml", package = "RDML7")
rdml <- readRDML(rdmlFile, showProgress = FALSE)

meta <- asTable(
  rdml,
  columns = c("position", "sample", "target", "adp"),
  cq = data$cq,
  namePattern = "{position}_{target}"
)
head(meta)

Serialize an RDML object to XML

Description

Serializes standard RDML properties. Package-only extension fields are kept in memory but are not emitted as non-standard XML elements.

Usage

asXML(x, ...)

Arguments

Value

Without 'fileName', a character scalar containing XML. With 'fileName', the serialized XML is returned invisibly after the file is written.

Arguments for the 'rdmlType' method

'fileName'

Optional output path. If omitted, return the complete XML document as a character scalar. A '.xml' path writes plain XML; other extensions, normally '.rdml', write a ZIP-based RDML archive.

'loss'

Policy for package data that standard RDML XML cannot represent: '"warn"' (default), '"error"', or '"allow"'.

See Also

'writeRDML()'

Examples

rdmlFile <- system.file("extdata", "lc96_bACTXY.rdml", package = "RDML7")
rdml <- readRDML(rdmlFile, showProgress = FALSE)

xml <- asXML(rdml, loss = "allow")
substr(xml, 1L, 80L)

output <- tempfile(fileext = ".xml")
invisible(asXML(rdml, fileName = output, loss = "allow"))
file.exists(output)
unlink(output)

Create an RDML object from fluorescence and metadata tables

Description

Create an RDML object from fluorescence and metadata tables

Usage

buildRDMLFromFData(
  fdata,
  description,
  fdataType = "adp",
  publisher = NULL,
  serialNumber = "1",
  ...
)

Arguments

Value

'rdmlType'.

See Also

'setFData', 'rdmlImportData'

Examples

rdmlFile <- system.file("extdata", "lc96_bACTXY.rdml", package = "RDML7")
source <- readRDML(rdmlFile, showProgress = FALSE)
description <- asTable(source)
description <- description[seq_len(min(2L, nrow(description))), ]
fluorescence <- getFData(source, request = description, dpType = "adp")

rebuilt <- buildRDMLFromFData(
  fdata = fluorescence,
  description = description,
  fdataType = "adp",
  publisher = "RDML7 example"
)
asTable(rebuilt)

Build rdmlType from canonical importer data

Description

Build rdmlType from canonical importer data

Usage

buildRDMLImport(importData, loss = c("warn", "error", "allow"), ...)

Arguments

Value

'rdmlType'.

See Also

'readRDML', 'rdmlImportData'

Examples

rdmlFile <- system.file("extdata", "lc96_bACTXY.rdml", package = "RDML7")
source <- readRDML(rdmlFile, showProgress = FALSE)
description <- asTable(source)
description <- description[seq_len(min(2L, nrow(description))), ]
fluorescence <- getFData(source, request = description, dpType = "adp")

series <- newRDMLImportSeries("adp", fluorescence, description)
importData <- newRDMLImportData(
  series = list(series),
  publisher = "RDML7 example",
  format = "rdml"
)
imported <- buildRDMLImport(importData, loss = "allow")
asTable(imported)

cdnaSynthesisMethodType S7 class

Description

Description of reverse-transcription/cDNA-synthesis conditions. Inherits from 'rdmlBaseType'.

Usage

cdnaSynthesisMethodType(
  enzyme = NA_character_,
  primingMethod = NA,
  dnaseTreatment = NA,
  thermalCyclingConditions = NA
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'cdnaSynthesisMethodType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'enzyme'

'character(1)' or 'NA'. Reverse-transcriptase/enzyme description.

'primingMethod'

'primingMethodType' or 'NA'. Priming strategy.

'dnaseTreatment'

'logical(1)' or 'NA'. Whether DNase treatment was performed.

'thermalCyclingConditions'

'idReferenceType' or 'NA'. Reference to the thermal program used for cDNA synthesis.

See Also

'primingMethodType', 'thermalCyclingConditionsType', 'sampleType'

commercialAssayType S7 class

Description

Commercial assay identification. Inherits from 'rdmlBaseType'.

Usage

commercialAssayType(company = character(0), orderNumber = character(0))

Arguments

Format

An S7 class.

Value

An S7 object of class 'commercialAssayType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'company'

'character(1)'. Manufacturer/company.

'orderNumber'

'character(1)'. Catalogue or order number.

See Also

'targetType'

cqDetectionMethodType S7 enumeration

Description

Method used to determine Cq values.

Usage

cqDetectionMethodType(value = "")

Arguments

Format

An S7 class.

Value

An S7 object of class 'cqDetectionMethodType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Allowed values

'automated threshold and baseline settings'

Allowed value.

'manual threshold and baseline settings'

Allowed value.

'second derivative maximum'

Allowed value.

'other'

Allowed value.

See Also

'runType', 'dataType'

dataCollectionSoftwareType S7 class

Description

Software used by the instrument to collect qPCR data. Inherits from 'rdmlBaseType'.

Usage

dataCollectionSoftwareType(name = character(0), version = character(0))

Arguments

Format

An S7 class.

Value

An S7 object of class 'dataCollectionSoftwareType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'name'

'character(1)'. Software name.

'version'

'character(1)'. Software version.

See Also

'runType'

dataType S7 class

Description

Target-specific qPCR result data for one reaction. It stores calculated results and optional amplification and melting fluorescence curves. Inherits from 'rdmlBaseType'.

Usage

dataType(
  targetId = NA,
  cq = NA_real_,
  N0 = NA_real_,
  ampEffMet = NA_character_,
  ampEff = NA_real_,
  ampEffSE = NA_real_,
  corrF = NA_real_,
  corrP = NA_real_,
  meltTemp = NA_real_,
  excl = NA_character_,
  note = NA_character_,
  adp = NA,
  mdp = NA,
  endPt = NA_real_,
  bgFluor = NA_real_,
  bgFluorSlp = NA_real_,
  quantFluor = NA_real_
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'dataType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'targetId'

'idReferenceType'. Reference to the target.

'cq'

'numeric(1)' or 'NA'. Quantification cycle (Cq).

'N0'

'numeric(1)' or 'NA'. Estimated initial template quantity.

'ampEffMet'

'character(1)' or 'NA'. Amplification-efficiency method.

'ampEff'

'numeric(1)' or 'NA'. Amplification efficiency.

'ampEffSE'

'numeric(1)' or 'NA'. Standard error of amplification efficiency.

'corrF'

'numeric(1)' or 'NA'. Fluorescence correction factor.

'corrP'

'numeric(1)' or 'NA'. Correction parameter.

'meltTemp'

Numeric vector or 'NA'. One or more melting temperatures.

'excl'

'character(1)' or 'NA'. Exclusion information.

'note'

'character(1)' or 'NA'. Free-text note.

'adp'

'dpAmpCurveType' or 'NA'. Amplification curve.

'mdp'

'dpMeltingCurveType' or 'NA'. Melting curve.

'endPt'

'numeric(1)' or 'NA'. End-point fluorescence/result.

'bgFluor'

'numeric(1)' or 'NA'. Background fluorescence.

'bgFluorSlp'

'numeric(1)' or 'NA'. Background-fluorescence slope.

'quantFluor'

'numeric(1)' or 'NA'. Quantification fluorescence.

See Also

'reactType', 'targetType', 'dpAmpCurveType', 'dpMeltingCurveType'

Detect the format handler selected for a path

Description

Detect the format handler selected for a path

Usage

detectRDMLFormat(fileName, operation = c("read", "write"))

Arguments

Value

Registered format name.

See Also

'listRDMLFormats', 'readRDML', 'writeRDML'

Examples

amplificationFile <- system.file(
  "extdata", "lc96_bACTXY.rdml", package = "RDML7"
)
meltingFile <- system.file(
  "extdata", "BioRad_qPCR_melt.rdml", package = "RDML7"
)
detectRDMLFormat(amplificationFile, operation = "read")
detectRDMLFormat(meltingFile, operation = "write")

documentationType S7 class

Description

Reusable documentation text. Use this type when the same description or note is referenced by several samples, targets, runs, or experiments. Inherits from 'rdmlBaseType'.

Usage

documentationType(id = NULL, text = NA_character_)

Arguments

Format

An S7 class.

Value

An S7 object of class 'documentationType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'id'

'idType'. Unique documentation identifier.

'text'

'character(1)' or 'NA'. Documentation text.

See Also

'rdmlType', 'idReferenceType'

dpAmpCurveType S7 class

Description

Amplification fluorescence curve. Inherits from 'rdmlBaseType'.

Usage

dpAmpCurveType(fpoints = NULL)

Arguments

Format

An S7 class.

Value

An S7 object of class 'dpAmpCurveType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'fpoints'

'data.table' containing 'cyc' and 'fluor', with optional per-cycle 'tmp'.

See Also

'dataType', 'getFData', 'setFData'

dpMeltingCurveType S7 class

Description

Melting fluorescence curve. Inherits from 'rdmlBaseType'.

Usage

dpMeltingCurveType(fpoints = NULL)

Arguments

Format

An S7 class.

Value

An S7 object of class 'dpMeltingCurveType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'fpoints'

'data.table' containing 'tmp' and 'fluor'.

See Also

'dataType', 'getFData', 'setFData'

dyeChemistryType S7 enumeration

Description

Fluorescence chemistry used by a dye or detection system.

Usage

dyeChemistryType(value = "")

Arguments

Format

An S7 class.

Value

An S7 object of class 'dyeChemistryType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Allowed values

'non-saturating DNA binding dye'

Allowed value.

'saturating DNA binding dye'

Allowed value.

'hybridization probe'

Allowed value.

'hydrolysis probe'

Allowed value.

'labelled forward primer'

Allowed value.

'labelled reverse primer'

Allowed value.

'DNA-zyme probe'

Allowed value.

See Also

'dyeType'

dyeType S7 class

Description

Description of a fluorescent dye or reporter used to detect a target. Inherits from 'rdmlBaseType'.

Usage

dyeType(id = NULL, description = NA_character_, dyeChemistry = NA)

Arguments

Format

An S7 class.

Value

An S7 object of class 'dyeType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'id'

'idType'. Unique dye identifier.

'description'

'character(1)' or 'NA'. Human-readable dye description.

'dyeChemistry'

'dyeChemistryType' or 'NA'. Detection chemistry.

See Also

'dyeChemistryType', 'targetType'

Launch the RDML editing interface

Description

Starts the optional Shiny-based editor when its GUI dependencies are installed.

Usage

editRDML()

Value

Result of launching the application, invisibly where applicable.

See Also

'readRDML', 'writeRDML'

experimentType S7 class

Description

A qPCR experiment. One experiment may contain several instrument runs. Inherits from 'rdmlBaseType'.

Usage

experimentType(
  id = NULL,
  description = NA_character_,
  documentation = NA,
  run = NA
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'experimentType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'id'

'idType'. Unique experiment identifier.

'description'

'character(1)' or 'NA'. Experiment description.

'documentation'

List of 'idReferenceType' objects or 'NA'. Documentation references.

'run'

Run-id-keyed list of 'runType' objects or 'NA'.

See Also

'runType', 'rdmlType'

experimenterType S7 class

Description

Contact details of an experimenter associated with an RDML document or thermal cycling conditions. Inherits from 'rdmlBaseType'.

Usage

experimenterType(
  id = NULL,
  firstName = character(0),
  lastName = character(0),
  email = NA_character_,
  labName = NA_character_,
  labAddress = NA_character_
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'experimenterType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'id'

'idType'. Unique experimenter identifier.

'firstName'

'character(1)'. First name.

'lastName'

'character(1)'. Last name.

'email'

'character(1)' or 'NA'. E-mail address.

'labName'

'character(1)' or 'NA'. Laboratory or organization name.

'labAddress'

'character(1)' or 'NA'. Laboratory postal address.

See Also

'rdmlType', 'thermalCyclingConditionsType'

Extract fluorescence data

Description

Extracts amplification or melting curves either from one [dataType] object or from a selection of curves in an [rdmlType] object.

Usage

getFData(x, ...)

Arguments

Value

A [data.table::data.table]. See **Output columns** for the shape returned by each method and argument combination.

Method arguments

'dpType'

Character scalar accepted by both methods: '"adp"' for amplification data or '"mdp"' for melting data. Defaults to '"adp"'.

'request'

For an 'rdmlType', a data frame normally produced by [asTable()]. It must contain 'fdataName', 'expId', 'runId', 'reactId', and 'target'. Additional columns are retained in long output. If omitted, 'asTable(x)' selects every stored target result.

'longTable'

For an 'rdmlType', return one row per measured point with request metadata repeated ('TRUE'), or a wide table with one fluorescence column per 'fdataName' ('FALSE', the default).

'includeMissing'

In long form, retain requested metadata rows that have no curve of the selected 'dpType', filling point columns with 'NA'? Defaults to 'FALSE'. It has no effect on wide output.

Output columns

For a single 'dataType', amplification output has 'cyc', optional 'tmp', and 'fluor'; melting output has 'tmp' and 'fluor'. A missing curve returns an empty table with the appropriate coordinate and 'fluor' columns.

For an 'rdmlType', wide amplification output begins with 'cyc' and may include 'tmp' when temperature is unambiguous for every cycle. Wide melting output begins with 'tmp'. Remaining columns are named by 'fdataName' in the order requested. Long output joins the request columns to 'cyc'/'tmp' and 'fluor'.

Duplicate 'fdataName' values are replaced by unique names constructed from 'expId', 'runId', 'reactId', and 'target', with a warning.

See Also

'asTable()', 'setFData()'

Examples

rdmlFile <- system.file("extdata", "lc96_bACTXY.rdml", package = "RDML7")
rdml <- readRDML(rdmlFile, showProgress = FALSE)
meta <- asTable(
  rdml,
  columns = c(
    "expId", "runId", "reactId", "position", "sample", "target", "adp"
  )
)

# All amplification curves as one wide table.
amplification <- getFData(rdml, dpType = "adp")

# Selected curves with metadata repeated for every cycle.
selected <- getFData(
  rdml,
  request = meta[seq_len(min(2L, nrow(meta))), ],
  dpType = "adp",
  longTable = TRUE
)

# Keep metadata even when melting data are absent.
melting <- getFData(
  rdml,
  request = meta,
  dpType = "mdp",
  longTable = TRUE,
  includeMissing = TRUE
)

gradientType S7 class

Description

Temperature-gradient step. Inherits from 'temperatureBaseType'.

Usage

gradientType(
  duration = integer(0),
  temperatureChange = NA_real_,
  durationChange = NA_integer_,
  measure = NA,
  ramp = NA_real_,
  highTemperature = integer(0),
  lowTemperature = integer(0)
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'gradientType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'highTemperature'

'numeric(1)'. High end of the gradient.

'lowTemperature'

'numeric(1)'. Low end of the gradient.

See Also

'temperatureBaseType', 'stepType'

RDML identifier reference

Description

Extends 'idType' for references between RDML elements, for example sample, target, dye, documentation, and thermal-program references.

Usage

idReferenceType(id = character(0))

Arguments

Value

An S7 object of class 'idReferenceType' representing a reference from one RDML schema element to another identified element.

See Also

'idType', 'validateRDML'

RDML identifier

Description

Stores one character identifier used as a schema key. 'as.character()' extracts the identifier and 'print()' displays it directly.

Usage

idType(id = character(0))

Arguments

Value

An S7 object of class 'idType' representing an identifier used as a key in the RDML object hierarchy.

See Also

'idReferenceType', 'rdmlKeyedList', 'rdmlType'

Test whether an RDML object has semantic errors

Description

Test whether an RDML object has semantic errors

Usage

isValidRDML(x, level = "full")

Arguments

Value

'TRUE' if no validation issue has severity '"error"'.

See Also

'validateRDML'

Examples

rdmlFile <- system.file(
  "extdata", "BioRad_qPCR_melt.rdml", package = "RDML7"
)
rdml <- readRDML(rdmlFile, showProgress = FALSE)

isValidRDML(rdml, level = "full")

labelFormatType S7 enumeration

Description

Labeling convention used for plate rows or columns.

Usage

labelFormatType(value = "")

Arguments

Format

An S7 class.

Value

An S7 object of class 'labelFormatType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Allowed values

'ABC'

Allowed value.

'123'

Allowed value.

'A1a1'

Allowed value.

See Also

'pcrFormatType'

Legacy API compatibility wrappers

Description

These functions preserve public names, dotted argument names, and (where applicable) dotted output-column names used by previous RDML releases. New code should use the canonical camelCase API.

Usage

AsTable(
  x,
  .default = list(exp.id = .rdmlIdChr(experiment$id), run.id = .rdmlIdChr(run$id),
    react.id = .rdmlIdChr(react$id), position = .rdmlReactPosition(react, run$pcrFormat),
    sample = .rdmlIdChr(react$sample), target = .rdmlIdChr(data$targetId), target.dyeId =
    .rdmlTargetDye(target, .rdmlIdChr(data$targetId)), sample.type =
    .rdmlSampleType(sample[[.rdmlIdChr(react$sample)]], .rdmlIdChr(data$targetId)), adp =
    .rdmlPresent(data$adp), mdp = .rdmlPresent(data$mdp)),
  name.pattern = paste(.rdmlIdChr(experiment$id), .rdmlIdChr(run$id),
    .rdmlReactPosition(react, run$pcrFormat), .rdmlIdChr(react$sample),
    .rdmlSampleType(sample[[.rdmlIdChr(react$sample)]], .rdmlIdChr(data$targetId)),
    .rdmlIdChr(data$targetId), sep = "_"),
  add.columns = list(),
  treat.null.as.na = FALSE,
  include.hidden = FALSE,
  ...
)

GetFData(x, request, dp.type = "adp", long.table = FALSE, ...)

SetFData(
  x,
  fdata,
  description,
  fdata.type = "adp",
  conflict = c("error", "keep", "replace"),
  ...
)

AsDendrogram(x, plot.dendrogram = TRUE, ...)

MergeRDMLs(to.merge, data.conflict = c("incoming", "base", "error"))

rdmlEdit(...)

Arguments

Details

Legacy 'AsTable()' returns names such as 'fdata.name', 'exp.id', 'run.id', 'react.id', 'sample.type', and 'target.dyeId'; 'asTable()' uses 'fdataName', 'expId', 'runId', 'reactId', 'sampleType', and 'targetDyeId'.

Value

'AsTable()' and 'GetFData()' return [data.table::data.table] objects with legacy dotted column names where applicable. 'SetFData()' and 'MergeRDMLs()' return [rdmlType] objects. 'AsDendrogram()' returns a 'dendrogram'. 'rdmlEdit()' launches the editor like [editRDML()].

See Also

[asTable()], [getFData()], [setFData()], [asDendrogram()], [mergeRDMLs()], [editRDML()], 'RDML7-package'

Examples

amplificationFile <- system.file(
  "extdata", "lc96_bACTXY.rdml", package = "RDML7"
)
meltingFile <- system.file(
  "extdata", "BioRad_qPCR_melt.rdml", package = "RDML7"
)
amplification <- readRDML(amplificationFile, showProgress = FALSE)
melting <- readRDML(meltingFile, showProgress = FALSE)

legacyMeta <- AsTable(amplification)
legacyCurves <- GetFData(
  amplification,
  request = legacyMeta[seq_len(min(2L, nrow(legacyMeta))), ],
  dp.type = "adp"
)
copied <- SetFData(
  rdmlType(),
  legacyCurves,
  legacyMeta[seq_len(min(2L, nrow(legacyMeta))), ],
  fdata.type = "adp"
)
tree <- AsDendrogram(melting, plot.dendrogram = FALSE)
merged <- MergeRDMLs(list(amplification, melting), data.conflict = "base")

lidOpenType S7 class

Description

Marker step indicating that the instrument lid is opened. This class has no additional properties. Inherits from 'rdmlBaseType'.

Usage

lidOpenType()

Format

An S7 class.

Value

An S7 object of class 'lidOpenType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

This class does not define additional properties.

See Also

'stepType'

List registered RDML file formats

Description

Formats are returned in registration order. For automatic dispatch, the first format supporting a given extension and operation is the default.

Usage

listRDMLFormats()

Value

Data frame with format name, extensions, and reader/writer availability.

See Also

'registerRDMLFormat', 'detectRDMLFormat'

Load file-format handlers from an R module

Description

The module defines 'rdmlModule()' (legacy 'rdml_module()' is also accepted) and returns one or more specifications accepted by 'registerRDMLFormat()'. Each specification may contain only 'name', 'extensions', 'reader', and 'writer'.

Usage

loadRDMLModule(path)

Arguments

Value

Registered format names invisibly.

See Also

'registerRDMLFormat', 'listRDMLFormats'

loopType S7 class

Description

Loop instruction in a thermal-cycling program. Inherits from 'rdmlBaseType'.

Usage

loopType(goto = integer(0), `repeat` = integer(0))

Arguments

Format

An S7 class.

Value

An S7 object of class 'loopType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'goto'

Positive integer. Number of the step to return to.

'repeat'

Positive integer. Number of loop repetitions.

See Also

'stepType', 'thermalCyclingConditionsType'

measureType S7 enumeration

Description

Fluorescence measurement mode used in a thermal-cycling step.

Usage

measureType(value = "")

Arguments

Format

An S7 class.

Value

An S7 object of class 'measureType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Allowed values

'real time'

Allowed value.

'meltcurve'

Allowed value.

See Also

'temperatureBaseType'

Merge multiple RDML objects

Description

Merge two or more [rdmlType] objects recursively.

Usage

mergeRDMLs(..., dataConflict = c("incoming", "base", "error"))

Arguments

Details

The **first** RDML object is used as the metadata base. Every subsequent object is merged into the accumulated result from left to right:

'mergeRDMLs(rdml1, rdml2, rdml3)' is therefore equivalent to 'merge(merge(rdml1, rdml2), rdml3)'.

The function accepts either RDML objects as separate arguments:

'mergeRDMLs(rdml1, rdml2, rdml3)'

or a single list containing RDML objects:

'mergeRDMLs(list(rdml1, rdml2, rdml3))'.

Top-level keyed metadata ('experimenter', 'documentation', 'dye', 'sample', 'target', and 'thermalCyclingConditions') keep the definition from the accumulated base object when the same key is present in both objects.

'dataConflict' applies to duplicate target data within the same reaction:

- '"incoming"': replace base data with data from the current incoming object. With multiple objects, later objects therefore have higher priority. - '"base"': preserve data already present in the accumulated base object. With multiple objects, earlier objects therefore have higher priority. - '"error"': stop at the first duplicate data target.

Value

Merged 'rdmlType'.

See Also

[readRDML()], [writeRDML()]

Examples

amplificationFile <- system.file(
  "extdata", "lc96_bACTXY.rdml", package = "RDML7"
)
meltingFile <- system.file(
  "extdata", "BioRad_qPCR_melt.rdml", package = "RDML7"
)

amplification <- readRDML(amplificationFile, showProgress = FALSE)
melting <- readRDML(meltingFile, showProgress = FALSE)

# Separate arguments
merged <- mergeRDMLs(
  amplification,
  melting,
  dataConflict = "error"
)

# A list is also accepted
mergedFromList <- mergeRDMLs(
  list(amplification, melting),
  dataConflict = "base"
)

Metadata schema types

Description

S7 classes representing reusable metadata elements in an RDML document.

Details

'experimenterType'

Experimenter/contact metadata: 'id', 'firstName', 'lastName', optional 'email', 'labName', and 'labAddress'.

'documentationType'

Reusable documentation identified by 'id' and optional free text.

'dyeChemistryType'

Enumeration describing fluorescence chemistry.

'dyeType'

Dye metadata: 'id', optional 'description', and optional 'dyeChemistry'.

'xRefType'

External cross-reference with optional 'name' and 'id'.

'annotationType'

Annotation 'property' / 'value' pair.

'rdmlIdType'

Top-level publisher identifier containing 'publisher', 'serialNumber', and optional 'MD5Hash'.

See Also

'idType', 'idReferenceType', 'rdmlType'

Create canonical importer data

Description

Create canonical importer data

Usage

newRDMLImportData(
  series,
  publisher = NA_character_,
  serialNumber = "1",
  format = NA_character_,
  preserveReactIds = FALSE,
  metadata = list(),
  losses = list()
)

Arguments

Value

'rdmlImportData'.

See Also

[newRDMLImportSeries()], [buildRDMLImport()]

Examples

rdmlFile <- system.file(
  "extdata", "BioRad_qPCR_melt.rdml", package = "RDML7"
)
rdml <- readRDML(rdmlFile, showProgress = FALSE)
description <- asTable(rdml)
description <- description[description$mdp %in% TRUE, ]
description <- description[seq_len(min(2L, nrow(description))), ]
fluorescence <- getFData(rdml, request = description, dpType = "mdp")
series <- newRDMLImportSeries("mdp", fluorescence, description)

importData <- newRDMLImportData(
  series = list(series),
  publisher = "Bio-Rad",
  serialNumber = "example",
  format = "rdml",
  metadata = list(source = basename(rdmlFile))
)
names(importData)

Create an importer fluorescence-series object

Description

Create an importer fluorescence-series object

Usage

newRDMLImportSeries(fdataType, fdata, description)

Arguments

Value

'rdmlImportSeries'.

See Also

[newRDMLImportData()], [buildRDMLImport()]

Examples

rdmlFile <- system.file("extdata", "lc96_bACTXY.rdml", package = "RDML7")
rdml <- readRDML(rdmlFile, showProgress = FALSE)
description <- asTable(rdml)
description <- description[seq_len(min(2L, nrow(description))), ]
fluorescence <- getFData(rdml, request = description, dpType = "adp")

series <- newRDMLImportSeries(
  fdataType = "adp",
  fdata = fluorescence,
  description = description
)
series$fdataType

Create a structured lossy-conversion record

Description

Importers/exporters use these records for information that cannot be represented exactly in the destination model.

Usage

newRDMLLossRecord(code, message, path = NA_character_, details = list())

Arguments

Value

An 'newRDMLLossRecord'.

See Also

'readRDML', 'writeRDML', 'rdmlImportData'

Examples

rdmlFile <- system.file(
  "extdata", "BioRad_qPCR_melt.rdml", package = "RDML7"
)
loss <- newRDMLLossRecord(
  code = "unsupportedMetadata",
  message = "Vendor metadata is retained only in the importer record",
  path = rdmlFile,
  details = list(format = detectRDMLFormat(rdmlFile, "read"))
)
loss

nucleotideType S7 enumeration

Description

Nucleic-acid type of the template material.

Usage

nucleotideType(value = "")

Arguments

Format

An S7 class.

Value

An S7 object of class 'nucleotideType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Allowed values

'DNA'

Allowed value.

'genomic DNA'

Allowed value.

'cDNA'

Allowed value.

'RNA'

Allowed value.

See Also

'templateQuantityType'

oligoType S7 class

Description

Oligonucleotide sequence used for a primer, probe, or amplicon definition. Inherits from 'rdmlBaseType'.

Usage

oligoType(
  threePrimeTag = NA_character_,
  fivePrimeTag = NA_character_,
  sequence = character(0)
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'oligoType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'threePrimeTag'

'character(1)' or 'NA'. Optional 3-prime modification/tag.

'fivePrimeTag'

'character(1)' or 'NA'. Optional 5-prime modification/tag.

'sequence'

'character(1)'. Nucleotide sequence.

See Also

'sequencesType'

partitionDataType S7 class

Description

Target-specific digital-PCR partition result data. Inherits from 'rdmlBaseType'.

Usage

partitionDataType(
  targetId = NA,
  excluded = NA_character_,
  note = NA_character_,
  pos = integer(0),
  neg = integer(0),
  undef = NA_integer_,
  excl = NA_integer_,
  conc = NA_real_
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'partitionDataType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'targetId'

'idReferenceType'. Reference to the target.

'excluded'

'character(1)' or 'NA'. Exclusion information.

'note'

'character(1)' or 'NA'. Note.

'pos'

Positive integer. Positive partitions.

'neg'

Positive integer. Negative partitions.

'undef'

Positive integer or 'NA'. Undefined partitions.

'excl'

Positive integer or 'NA'. Excluded partitions.

'conc'

'numeric(1)' or 'NA'. Calculated concentration.

See Also

'partitionsType', 'targetType'

partitionsType S7 class

Description

Digital-PCR partition metadata and target-specific partition results. Inherits from 'rdmlBaseType'.

Usage

partitionsType(volume = integer(0), endPtTable = NA_character_, data = NA)

Arguments

Format

An S7 class.

Value

An S7 object of class 'partitionsType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'volume'

'numeric(1)'. Partition volume.

'endPtTable'

'character(1)' or 'NA'. Optional endpoint-table representation/reference.

'data'

Target-keyed list of 'partitionDataType' objects or 'NA'.

See Also

'partitionDataType', 'reactType'

pauseType S7 class

Description

Pause instruction at a specified temperature. Inherits from 'rdmlBaseType'.

Usage

pauseType(temperature = integer(0))

Arguments

Format

An S7 class.

Value

An S7 object of class 'pauseType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'temperature'

'numeric(1)'. Pause temperature.

See Also

'stepType'

pcrFormatType S7 class

Description

PCR plate or reaction-layout dimensions and labeling conventions. Inherits from 'rdmlBaseType'.

Usage

pcrFormatType(
  rows = integer(0),
  columns = integer(0),
  rowLabel = NA,
  columnLabel = NA
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'pcrFormatType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'rows'

Positive integer. Number of rows.

'columns'

Positive integer. Number of columns.

'rowLabel'

'labelFormatType'. Row-label convention.

'columnLabel'

'labelFormatType'. Column-label convention.

See Also

'labelFormatType', 'runType'

primingMethodType S7 enumeration

Description

Priming strategy used for cDNA synthesis.

Usage

primingMethodType(value = "")

Arguments

Format

An S7 class.

Value

An S7 object of class 'primingMethodType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Allowed values

'oligo-dt'

Allowed value.

'random'

Allowed value.

'target-specific'

Allowed value.

'oligo-dt and random'

Allowed value.

'other'

Allowed value.

See Also

'cdnaSynthesisMethodType'

quantityType S7 class

Description

Target-specific quantity assigned to a sample. Inherits from 'rdmlBaseType'.

Usage

quantityType(targetId = NA, value = integer(0), unit = quantityUnitType())

Arguments

Format

An S7 class.

Value

An S7 object of class 'quantityType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'targetId'

'idReferenceType'. Reference to the target.

'value'

'numeric(1)'. Quantity value.

'unit'

'quantityUnitType'. Unit of the quantity.

See Also

'sampleType', 'quantityUnitType'

quantityUnitType S7 enumeration

Description

Unit used for a target-specific sample quantity.

Usage

quantityUnitType(value = "")

Arguments

Format

An S7 class.

Value

An S7 object of class 'quantityUnitType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Allowed values

'cop'

copies.

'fold'

fold value.

'dil'

dilution.

'ng'

nanograms.

'nMol'

nanomoles.

'other'

another unit.

See Also

'quantityType'

Experimental data and run schema types

Description

S7 classes for fluorescence curves, reactions, runs, experiments, plate layouts, digital-PCR partitions, and the top-level RDML document.

Curve and result classes

'dpAmpCurveType'

Amplification 'fpoints': 'cyc', optional 'tmp', and 'fluor'.

'dpMeltingCurveType'

Melting 'fpoints': 'tmp' and 'fluor'.

'dataType'

Target-specific results and curves.

Hierarchy and layout

'partitionDataType', 'partitionsType'

Digital-PCR partition data.

'reactType'

Reaction with sample reference and target-keyed data.

'dataCollectionSoftwareType'

Software name/version.

'labelFormatType'

Plate label enumeration.

'pcrFormatType'

Plate dimensions and label formats.

'cqDetectionMethodType'

Cq-detection method enumeration.

'runType'

Instrument run and reactions.

'experimentType'

Experiment and runs.

'rdmlType'

Top-level RDML document.

Sample and target schema types

Description

S7 classes used to describe samples, quantities, targets, oligonucleotides, assays, and cDNA synthesis metadata.

Enumerations

'sampleTypeType'

'unkn', 'ntc', 'nac', 'std', 'ntp', 'nrt', 'pos', or 'opt'.

'quantityUnitType'

'cop', 'fold', 'dil', 'ng', 'nMol', or 'other'.

'primingMethodType'

'oligo-dt', 'random', 'target-specific', 'oligo-dt and random', or 'other'.

'nucleotideType'

'DNA', 'genomic DNA', 'cDNA', or 'RNA'.

'targetTypeType'

'ref' or 'toi'.

Classes

'sampleTargetType'

Associates 'targetId' with a sample type.

'quantityType'

Target-specific quantity: 'targetId', 'value', and 'unit'.

'cdnaSynthesisMethodType'

Enzyme, priming method, DNase treatment, and optional thermal-program reference.

'templateQuantityType'

Template concentration and nucleotide type.

'sampleType'

Sample metadata, target-specific type/quantity, annotations, documentation, and cDNA synthesis information.

'oligoType'

Oligonucleotide sequence and optional terminal tags.

'sequencesType'

Primers, probes, and optional amplicon sequence.

'commercialAssayType'

Commercial assay company and order number.

'targetType'

Target type, dye reference, amplification efficiency, optional sequences, and commercial assay metadata.

Thermal-cycling schema types

Description

S7 types used to represent PCR and melting thermal programs.

Details

'measureType' accepts 'real time' or 'meltcurve'.

'temperatureBaseType'

Common duration, measurement, ramp, and change fields.

'temperatureType'

Fixed-temperature step.

'gradientType'

Gradient step with high/low temperatures.

'loopType'

Loop control with 'goto' and 'repeat'.

'pauseType'

Pause at a temperature.

'lidOpenType'

Marker step indicating an open lid.

'stepType'

Numbered step containing one thermal action.

'thermalCyclingConditionsType'

Named thermal program containing 'stepType' objects.

rdmlIdType S7 class

Description

Publisher identifier for an RDML document. Inherits from 'rdmlBaseType'.

Usage

rdmlIdType(
  publisher = character(0),
  serialNumber = character(0),
  MD5Hash = NA_character_
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'rdmlIdType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'publisher'

'character(1)'. Publisher/producer identifier.

'serialNumber'

'character(1)'. Serial number assigned by the publisher.

'MD5Hash'

'character(1)' or 'NA'. Optional MD5 hash.

See Also

'rdmlType'

Parsed importer data before construction of rdmlType

Description

Decouples vendor parsing from construction of the nested RDML hierarchy. 'readRDML()' builds this representation centrally with 'buildRDMLImport()'.

Usage

rdmlImportData(
  series,
  publisher = NA_character_,
  serialNumber = "1",
  format = NA_character_,
  preserveReactIds = FALSE,
  metadata = list(),
  losses = list()
)

Arguments

Value

An S7 object of class 'rdmlImportData' containing normalized amplification and melting series together with source metadata and loss records, ready for construction of an RDML document.

See Also

'rdmlImportSeries', 'buildRDMLImport', 'registerRDMLFormat'

One fluorescence-series group for the importer API

Description

Intermediate representation used by table/vendor parsers.

Usage

rdmlImportSeries(fdataType = character(0), fdata = NULL, description = NULL)

Arguments

Value

An S7 object of class 'rdmlImportSeries' containing one normalized fluorescence series and its associated experiment, run, reaction, sample, and target metadata.

See Also

'rdmlImportData', 'buildRDMLImport'

Keyed list view used by RDML S7 objects

Description

Derives virtual element names from a property such as 'id' or 'targetId' and enables nested '$' / '[[' access without storing physical list names.

Usage

rdmlKeyedList(x = list(), key = "id")

Arguments

Value

An 'rdmlKeyedList' S7 object.

See Also

'rdmlType', 'idType'

rdmlType S7 class

Description

Top-level container representing one RDML document. Its structure mirrors the RDML schema and stores reusable metadata together with experiments and runs. Inherits from 'rdmlBaseType'.

Usage

rdmlType(
  dateMade = NA_character_,
  dateUpdated = NA_character_,
  id = NA,
  experimenter = NA,
  documentation = NA,
  dye = NA,
  sample = NA,
  target = NA,
  thermalCyclingConditions = NA,
  experiment = NA
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'rdmlType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'version'

'character(1)'. RDML schema version represented by this object. Always '"1.3"' and read-only.

'dateMade'

Date-time value or 'NA'. Document creation date.

'dateUpdated'

Date-time value or 'NA'. Last update date.

'id'

List of 'rdmlIdType' objects or 'NA'. Publisher identifiers.

'experimenter'

Experimenter-id-keyed list of 'experimenterType' objects or 'NA'.

'documentation'

Documentation-id-keyed list of 'documentationType' objects or 'NA'.

'dye'

Dye-id-keyed list of 'dyeType' objects or 'NA'.

'sample'

Sample-id-keyed list of 'sampleType' objects or 'NA'.

'target'

Target-id-keyed list of 'targetType' objects or 'NA'.

'thermalCyclingConditions'

Id-keyed list of 'thermalCyclingConditionsType' objects or 'NA'.

'experiment'

Experiment-id-keyed list of 'experimentType' objects or 'NA'.

See Also

'readRDML', 'writeRDML', 'asTable', 'getFData', 'validateRDML'

Return the canonical position of an RDML reaction

Description

Converts the schema-level reaction identifier to a human-readable plate position using the run PCR format. Conventional alphabetic-row positions always use two-digit columns (for example, 'A01', never 'A1').

Usage

reactPosition(react, pcrFormat = NULL)

Arguments

Value

A character scalar containing the canonical reaction position.

reactType S7 class

Description

One reaction/well within a run. It references a sample and stores target-specific qPCR or digital-PCR results. Inherits from 'rdmlBaseType'.

Usage

reactType(id = NULL, sample = NA, data = NA, partitions = NA)

Arguments

Format

An S7 class.

Value

An S7 object of class 'reactType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'id'

'idType'. Reaction identifier or well position.

'sample'

'idReferenceType'. Reference to the sample.

'data'

Target-keyed list of 'dataType' objects or 'NA'.

'partitions'

List of 'partitionsType' objects or 'NA'.

See Also

'runType', 'sampleType', 'dataType', 'partitionsType'

Read qPCR data into an RDML object

Description

Selects a reader from the runtime registry. Readers may return 'rdmlType' directly or 'rdmlImportData', which is built automatically.

Usage

readRDML(
  fileName,
  showProgress = TRUE,
  conditionsSep = NULL,
  cluster = NULL,
  format = "auto",
  loss = c("warn", "error", "allow"),
  ...
)

Arguments

Value

'rdmlType'.

See Also

'writeRDML', 'listRDMLFormats', 'validateRDML'

Register a file-format reader and/or writer

Description

Register a named file format. Automatic dispatch uses the file extension. If several formats support the same extension and operation, the first registered matching format is used by default. Users can select another registered format explicitly with 'format = "name"'.

Usage

registerRDMLFormat(
  name,
  extensions = character(),
  reader = NULL,
  writer = NULL
)

Arguments

Value

Registered format specification invisibly.

See Also

'loadRDMLModule', 'listRDMLFormats', 'readRDML'

Examples

rdmlFile <- system.file("extdata", "lc96_bACTXY.rdml", package = "RDML7")
demoFile <- tempfile(fileext = ".rdmldemo")
file.copy(rdmlFile, demoFile)

registerRDMLFormat(
  name = "rdml-demo",
  extensions = "rdmldemo",
  reader = function(fileName, ...) {
    readRDML(fileName, format = "rdml", ...)
  }
)
detectRDMLFormat(demoFile, "read")
demo <- readRDML(demoFile, showProgress = FALSE)

unregisterRDMLFormat("rdml-demo")
unlink(demoFile)

runType S7 class

Description

One qPCR instrument run within an experiment. A run contains instrument/acquisition metadata and reactions. Inherits from 'rdmlBaseType'.

Usage

runType(
  id = NULL,
  description = NA_character_,
  documentation = NA,
  experimenter = NA,
  instrument = NA_character_,
  dataCollectionSoftware = NA,
  backgroundDeterminationMethod = NA_character_,
  cqDetectionMethod = NA,
  thermalCyclingConditions = NA,
  pcrFormat = NA,
  runDate = NA_character_,
  react = NA
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'runType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'id'

'idType'. Unique run identifier within the experiment.

'description'

'character(1)' or 'NA'. Run description.

'documentation'

List of 'idReferenceType' objects or 'NA'. Documentation references.

'experimenter'

List of 'idReferenceType' objects or 'NA'. Experimenter references.

'instrument'

'character(1)' or 'NA'. Instrument description.

'dataCollectionSoftware'

'dataCollectionSoftwareType' or 'NA'. Acquisition software.

'backgroundDeterminationMethod'

'character(1)' or 'NA'. Background determination method.

'cqDetectionMethod'

'cqDetectionMethodType' or 'NA'. Cq calculation method.

'thermalCyclingConditions'

'idReferenceType' or 'NA'. Reference to thermal cycling conditions.

'pcrFormat'

'pcrFormatType' or 'NA'. Plate/layout format.

'runDate'

Date-time value or 'NA'. Date/time of the run.

'react'

Reaction-id-keyed list of 'reactType' objects or 'NA'.

See Also

'experimentType', 'reactType', 'pcrFormatType', 'thermalCyclingConditionsType'

sampleTargetType S7 class

Description

Sample role, optionally restricted to a target. If 'targetId' is 'NA', the role applies to all targets unless a target-specific role overrides it. Inherits from 'rdmlBaseType'.

Usage

sampleTargetType(targetId = NA, sampleType = sampleTypeType())

Arguments

Format

An S7 class.

Value

An S7 object of class 'sampleTargetType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'targetId'

'idReferenceType' or 'NA'. Optional target reference; 'NA' means that the sample role is target-independent.

'sampleType'

'sampleTypeType'. Role of the sample for that target.

See Also

'sampleTypeType', 'sampleType', 'targetType'

sampleType S7 class

Description

A qPCR sample/template solution. Dilutions with different concentrations are represented as different samples; technical replicates normally reference the same sample id, while biological replicates normally use different sample ids. Inherits from 'rdmlBaseType'.

Usage

sampleType(
  id = NULL,
  description = NA_character_,
  documentation = NA,
  xRef = NA,
  annotation = NA,
  type = NA,
  interRunCalibrator = NA,
  quantity = NA,
  calibratorSample = NA,
  cdnaSynthesisMethod = NA,
  templateQuantity = NA
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'sampleType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'id'

'idType'. Unique sample identifier.

'description'

'character(1)' or 'NA'. Sample description.

'documentation'

List of 'idReferenceType' objects or 'NA'. References to reusable documentation.

'xRef'

List of 'xRefType' objects or 'NA'. External references.

'annotation'

List of 'annotationType' objects or 'NA'. Sample annotations.

'type'

List of 'sampleTargetType' objects or 'NA'. Roles may be target-independent or target-specific.

'interRunCalibrator'

'logical(1)' or 'NA'. Marks an inter-run calibrator.

'quantity'

Target-keyed list of 'quantityType' objects or 'NA'. Target-specific quantities.

'calibratorSample'

'logical(1)' or 'NA'. Marks a calibrator sample.

'cdnaSynthesisMethod'

'cdnaSynthesisMethodType' or 'NA'. cDNA synthesis metadata.

'templateQuantity'

'templateQuantityType' or 'NA'. Template concentration/type.

See Also

'sampleTargetType', 'quantityType', 'reactType', 'rdmlType'

sampleTypeType S7 enumeration

Description

Role of a sample for a particular target.

Usage

sampleTypeType(value = "")

Arguments

Format

An S7 class.

Value

An S7 object of class 'sampleTypeType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Allowed values

'unkn'

unknown sample.

'ntc'

no-template control.

'nac'

no-amplification control.

'std'

standard.

'ntp'

no-target-positive control.

'nrt'

no-reverse-transcription control.

'pos'

positive control.

'opt'

optical calibrator.

See Also

'sampleTargetType', 'sampleType'

sequencesType S7 class

Description

Primer, probe, and amplicon sequences associated with a target. Inherits from 'rdmlBaseType'.

Usage

sequencesType(
  forwardPrimer = NA,
  reversePrimer = NA,
  probe1 = NA,
  probe2 = NA,
  amplicon = NA
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'sequencesType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'forwardPrimer'

'oligoType' or 'NA'. Forward primer.

'reversePrimer'

'oligoType' or 'NA'. Reverse primer.

'probe1'

'oligoType' or 'NA'. First probe.

'probe2'

'oligoType' or 'NA'. Second probe.

'amplicon'

'oligoType' or 'NA'. Amplicon sequence.

See Also

'oligoType', 'targetType'

Add or replace fluorescence data

Description

Adds wide fluorescence data and its metadata to an [rdmlType]. Missing experiments, runs, reactions, samples, targets, and dyes are created when enough metadata are supplied.

Usage

setFData(x, ...)

Arguments

Details

New runs receive a conventional 96-well format, or a 384-well format when numeric reaction identifiers exceed 96. Each fluorescence column must have exactly one matching description row; undescribed columns are skipped with a warning and duplicate descriptions are an error.

RDML objects use value semantics: this function does not modify 'x' in place. Assign the returned value.

Value

The updated [rdmlType] object.

Arguments for the 'rdmlType' method

'fdata'

A matrix, data frame, or [data.table::data.table]. The first column contains the coordinate ('cyc' for amplification or 'tmp' for melting); every other fluorescence column is matched to a row of 'description' through 'fdataName'. For amplification data, an optional column named 'tmp' is stored as per-cycle temperature unless explicitly described as a fluorescence series.

'description'

A metadata table with one row per fluorescence column. Required columns are 'fdataName', 'expId', 'runId', 'reactId', and 'target'. 'sample' is required when creating a new reaction, and 'targetDyeId' is required when creating a new target. Recognized optional columns include 'sampleType', 'targetType', 'cq', 'meltTemp', and 'quantity'.

'fdataType'

Character scalar: '"adp"' for amplification data or '"mdp"' for melting data. Defaults to '"adp"'.

'conflict'

How to handle metadata that disagree with existing RDML objects: '"error"' (default) stops, '"keep"' retains existing metadata, and '"replace"' updates it. Fluorescence curves supplied in 'fdata' are written for their selected 'fdataType'.

See Also

'buildRDMLFromFData()', 'asTable()', 'getFData()'

Examples

rdmlFile <- system.file("extdata", "lc96_bACTXY.rdml", package = "RDML7")
source <- readRDML(rdmlFile, showProgress = FALSE)
metadata <- asTable(source)
metadata <- metadata[seq_len(min(2L, nrow(metadata))), ]
curves <- getFData(
  source,
  request = metadata,
  dpType = "adp"
)

copied <- setFData(
  rdmlType(),
  fdata = curves,
  description = metadata,
  fdataType = "adp"
)
asTable(copied)

stepType S7 class

Description

One numbered step of a thermal-cycling program. Exactly one of the action properties normally describes the operation performed by the step. Inherits from 'rdmlBaseType'.

Usage

stepType(
  nr = integer(0),
  description = NA_character_,
  temperature = NA,
  gradient = NA,
  loop = NA,
  pause = NA,
  lidOpen = NA
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'stepType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'nr'

Positive integer. Step number.

'description'

'character(1)' or 'NA'. Step description.

'temperature'

'temperatureType' or 'NA'. Fixed-temperature action.

'gradient'

'gradientType' or 'NA'. Gradient action.

'loop'

'loopType' or 'NA'. Loop action.

'pause'

'pauseType' or 'NA'. Pause action.

'lidOpen'

'lidOpenType' or 'NA'. Lid-open action.

See Also

'thermalCyclingConditionsType', 'temperatureType', 'gradientType', 'loopType'

Summarize an RDML object

Description

Provides a compact structural summary of an [rdmlType] object.

Usage

## S7 method for class <RDML7::rdmlType>
summary(object, ...)

Arguments

Details

'summary()' reports the RDML version and dates together with counts of experiments, runs, reactions, data elements, samples, targets, dyes, thermal cycling conditions, amplification curves ('adp'), and melting curves ('mdp').

The historical 'totalMultiTm' field is no longer calculated or returned.

Value

An object of class 'summary.rdmlType'.

Examples

rdmlFile <- system.file("extdata", "lc96_bACTXY.rdml", package = "RDML7")
rdml <- readRDML(rdmlFile, showProgress = FALSE)
summary(rdml)

targetType S7 class

Description

Description of a qPCR target, including dye, efficiency, sequence, and assay metadata. Inherits from 'rdmlBaseType'.

Usage

targetType(
  id = NULL,
  description = NA_character_,
  documentation = NA,
  xRef = NA,
  type = NA,
  amplificationEfficiencyMethod = NA_character_,
  amplificationEfficiency = NA_real_,
  amplificationEfficiencySE = NA_real_,
  meltingTemperature = NA_real_,
  detectionLimit = NA_real_,
  dyeId = NA,
  sequences = NA,
  commercialAssay = NA
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'targetType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'id'

'idType'. Unique target identifier.

'description'

'character(1)' or 'NA'. Target description.

'documentation'

List of 'idReferenceType' objects or 'NA'. Documentation references.

'xRef'

List of 'xRefType' objects or 'NA'. External references.

'type'

'targetTypeType'. Reference target or target of interest.

'amplificationEfficiencyMethod'

'character(1)' or 'NA'. Method used to determine amplification efficiency.

'amplificationEfficiency'

'numeric(1)' or 'NA'. Amplification efficiency.

'amplificationEfficiencySE'

'numeric(1)' or 'NA'. Standard error of amplification efficiency.

'meltingTemperature'

'numeric(1)' or 'NA'. Expected target melting temperature.

'detectionLimit'

'numeric(1)' or 'NA'. Detection limit.

'dyeId'

'idReferenceType'. Reference to the detection dye.

'sequences'

'sequencesType' or 'NA'. Primers/probes/amplicon.

'commercialAssay'

'commercialAssayType' or 'NA'. Commercial assay metadata.

See Also

'targetTypeType', 'dyeType', 'dataType', 'rdmlType'

targetTypeType S7 enumeration

Description

Functional role of a target.

Usage

targetTypeType(value = "")

Arguments

Format

An S7 class.

Value

An S7 object of class 'targetTypeType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Allowed values

'ref'

reference target.

'toi'

target of interest.

See Also

'targetType'

temperatureBaseType S7 class

Description

Base class for thermal steps with duration, measurement, ramp, and per-cycle changes. Inherits from 'rdmlBaseType'.

Usage

temperatureBaseType(
  duration = integer(0),
  temperatureChange = NA_real_,
  durationChange = NA_integer_,
  measure = NA,
  ramp = NA_real_
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'temperatureBaseType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'duration'

Positive integer. Step duration.

'temperatureChange'

'numeric(1)' or 'NA'. Temperature increment/decrement per cycle.

'durationChange'

'integer(1)' or 'NA'. Duration increment/decrement per cycle.

'measure'

'measureType' or 'NA'. Fluorescence measurement mode.

'ramp'

'numeric(1)' or 'NA'. Ramp rate.

See Also

'temperatureType', 'gradientType', 'measureType'

temperatureType S7 class

Description

Fixed-temperature thermal-cycling step. Inherits from 'temperatureBaseType'.

Usage

temperatureType(
  duration = integer(0),
  temperatureChange = NA_real_,
  durationChange = NA_integer_,
  measure = NA,
  ramp = NA_real_,
  temperature = integer(0)
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'temperatureType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'temperature'

'numeric(1)'. Step temperature.

See Also

'temperatureBaseType', 'stepType'

templateQuantityType S7 class

Description

Total template concentration together with the template nucleotide type. Inherits from 'rdmlBaseType'.

Usage

templateQuantityType(conc = integer(0), nucleotide = nucleotideType())

Arguments

Format

An S7 class.

Value

An S7 object of class 'templateQuantityType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'conc'

'numeric(1)'. Template concentration.

'nucleotide'

'nucleotideType'. Nucleic-acid type.

See Also

'nucleotideType', 'sampleType'

thermalCyclingConditionsType S7 class

Description

A reusable thermal-cycling program referenced by runs or cDNA-synthesis metadata. Inherits from 'rdmlBaseType'.

Usage

thermalCyclingConditionsType(
  id = NULL,
  description = NA_character_,
  documentation = NA,
  lidTemperature = NA_real_,
  experimenter = NA,
  step = list()
)

Arguments

Format

An S7 class.

Value

An S7 object of class 'thermalCyclingConditionsType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'id'

'idType'. Unique program identifier.

'description'

'character(1)' or 'NA'. Program description.

'documentation'

List of 'idReferenceType' objects or 'NA'. Documentation references.

'lidTemperature'

'numeric(1)' or 'NA'. Heated-lid temperature.

'experimenter'

List of 'idReferenceType' objects or 'NA'. Experimenter references.

'step'

List of 'stepType' objects. Ordered program steps.

See Also

'stepType', 'runType', 'cdnaSynthesisMethodType'

Unregister a file format

Description

Unregister a file format

Usage

unregisterRDMLFormat(name, force = FALSE)

Arguments

Value

'TRUE' invisibly when removed.

See Also

'registerRDMLFormat', 'listRDMLFormats'

Semantically validate an RDML object

Description

Checks duplicate keys, dangling references, and fluorescence-curve consistency in addition to S7 property validation.

Usage

validateRDML(
  x,
  level = c("full", "structure", "references", "data"),
  action = c("return", "warn", "error")
)

Arguments

Value

A 'data.table' of class 'rdmlValidation' describing issues.

See Also

'isValidRDML', 'rdmlSummary'

Examples

rdmlFile <- system.file("extdata", "lc96_bACTXY.rdml", package = "RDML7")
rdml <- readRDML(rdmlFile, showProgress = FALSE)

issues <- validateRDML(rdml, level = "full", action = "return")
issues

Write an RDML object through the file-format registry

Description

Write an RDML object through the file-format registry

Usage

writeRDML(
  x,
  fileName,
  format = "auto",
  overwrite = FALSE,
  loss = c("warn", "error", "allow"),
  ...
)

Arguments

Value

Writer-specific result, normally an output path invisibly.

See Also

'readRDML', 'listRDMLFormats', 'newRDMLLossRecord'

xRefType S7 class

Description

External database or ontology cross-reference. Inherits from 'rdmlBaseType'.

Usage

xRefType(name = NA_character_, id = NA_character_)

Arguments

Format

An S7 class.

Value

An S7 object of class 'xRefType' representing the documented RDML schema element. Constructor arguments and object properties describe the element's structure and meaning.

Properties

'name'

'character(1)' or 'NA'. Name of the external reference system.

'id'

'character(1)' or 'NA'. Identifier in that reference system.

See Also

'sampleType', 'targetType'