Differential Pattern Analysis via Linear Modeling

Documentation for package ‘DiPALM’ version 1.3

DiPALM-package	DiPALM - Differential Pattern Analysis via Linear Modeling
AdjustPvalue	Determine p-values based on permutation test results
BlankPlot	Generate a blank plot window
BuildLimmaLM	Fit linear models to time-course expression patterns using the limma package
BuildModMembership	Calculate module membership (kME) for all genes in a time-course data set
col_format_sub	Substitute values in for the time, treatment, and replicate portion of a column format.
DiPALM	DiPALM - Differential Pattern Analysis via Linear Modeling
dipalm	Run a single instance of the DiPALM pipeline with replicates permuted.
exampleData	Example Data: Data for use with the DiPALM vignette
ggPlotMultiDensities	Plot multiple density distributions
joinOutputs	Joins outputs from multiple invocations of the function 'dipalm'.
main	Runs the full DiPALM pipeline with replicate permutation in parallel.
make_TCs	Break a data matrix into time courses separated by treatment and replicate.
msub	Regex substitution applied to a vector or list.
open_log	Open a log
PlotTCs	Plot multiple time-course expression patterns for one gene
PlotTCsRibbon	Plot multiple averaged time-course expression patterns for a group of genes
re_esc	Format a string as a regular expression literal.
sampleReplicates	Samples replicates from a dataset without replacement.
smallTestData	Small test data for the DiPALM pipeline.
testData	Test Data: Data for function testing