affxparser (version 1.44.0)

readBpmap: Parses a Bpmap file

Description

Parses (parts of) a Bpmap (binary probe mapping) file from Affymetrix.

Usage

readBpmap(filename, seqIndices = NULL, readProbeSeq = TRUE, readSeqInfo = TRUE, readPMXY = TRUE, readMMXY = TRUE, readStartPos = TRUE, readCenterPos = FALSE, readStrand = TRUE, readMatchScore = FALSE, readProbeLength = FALSE, verbose = 0)
readBpmapHeader(filename)
readBpmapSeqinfo(filename, seqIndices = NULL, verbose = 0)

Arguments

filename
The filename as a character.
seqIndices
A vector of integers, detailing the indices of the sequences being read. If NULL, the entire file is being read.
readProbeSeq
Do we read the probe sequences.
readSeqInfo
Do we read the sequence information (a list containing information such as sequence name, number of hits etc.)
readPMXY
Do we read the (x,y) coordinates of the PM-probes.
readMMXY
Do we read the (x,y) coordinates of the MM-probes (only relevant if the file has MM information)
readStartPos
Do we read the start position of the probes.
readCenterPos
Do we return the start position of the probes.
readStrand
Do we return the strand of the hits.
readMatchScore
Do we return the matchscore.
readProbeLength
Doe we return the probelength.
verbose
How verbose do we want to be.

Value

For readBpmap: A list of lists, one list for every sequence read. The components of the sequence lists, depends on the argument of the function call. For readBpmapheader a list with two components version and numSequences. For readBpmapSeqinfo a list of lists containing the sequence info.

Details

readBpmap reads a BPMAP file, which is a binary file containing information about a given probe's location in a sequence. Here sequence means some kind of reference sequence, typically a chromosome or a scaffold. readBpmapHeader reads the header of the BPMAP file, and readBpmapSeqinfo reads the sequence info of the sequences (so this function is merely a convinience function).

See Also

tpmap2bpmap for information on how to write Bpmap files.