readBpmap: Parses a Bpmap file

Description Usage Arguments Details Value Author(s) See Also

View source: R/readBpmap.R

Description

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

Usage

1
2
3
4
5
6
7
8
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.


affxparser documentation built on Nov. 1, 2018, 2:25 a.m.