readBpmap: Parses a Bpmap file
In affxparser: Affymetrix File Parsing SDK

Description Usage Arguments Details Value Author(s) See Also

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

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)

`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.

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).

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.

Kasper Daniel Hansen

tpmap2bpmap for information on how to write Bpmap files.

affxparser documentation built on Nov. 8, 2020, 7:26 p.m.