| read.abif {seqinr} | R Documentation |
ABIF stands for Applied Biosystem Inc. Format, a binary fromat modeled after TIFF format.
Corresponding files usually have an *.ab1 or *.fsa extension.
read.abif(filename, max.bytes.in.file = file.info(filename)$size, pied.de.pilote = 1.2, verbose = FALSE)
filename |
The name of the file. |
max.bytes.in.file |
The size in bytes of the file, defaulting to what is returned by file.info |
pied.de.pilote |
Safety factor: the argument n to readBin is set as pied.de.pilote*max.bytes.in.file. |
verbose |
logical [FALSE]. If TRUE verbose mode is on. |
This function is experiemental and has not been intensively tested. All data are imported into memory, there is no attempt to read items on the fly.
A list with three components: Header which is a list that contains various low-level information,
among which numelements is the number of elements in the directory and dataoffset
the offset to find the location of the directory. Directory is a data.frame for the directory
of the file with the number of row being the number of elements in the directory and the 7
columns describing various low-level information about the elements. Data is a list
with the number of components equal to the number of elements in the directory.
J.R. Lobry
citation("seqinR")
Anonymous (2006) Applied Biosystem Genetic Analysis Data File Format. Available at http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf. Last visited on 03-NOV-2008.
readBin which is used here to import the binary file and file.info to
get the size of the file.
# Quality check:
data(JLO)
JLO.check <- read.abif(system.file("abif/2_FAC321_0000205983_B02_004.fsa",
package = "seqinr"))
stopifnot(identical(JLO, JLO.check))