readBpmap {affxparser}R Documentation

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
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 convinience 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.

Note

Author(s)

Kasper Daniel Hansen <khansen@stat.berkeley.edu>

References

See Also

tpmap2bpmap for information on how to write Bpmap files.

Examples






[Package affxparser version 1.10.2 Index]