readBpmap: Parses a Bpmap file

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

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.

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 convenience function).

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.

Author(s)

Kasper Daniel Hansen

See Also

tpmap2bpmap for information on how to write Bpmap files.

HenrikBengtsson/affxparser documentation built on Feb. 9, 2024, 3:13 a.m.