RMAT (version 3.22.0)

ReadBPMAPAllSeqHeader: Reading All the BPMAP Sequence Header

Description

Reading the header of a specified sequence in the BPMAP file. Several sequences could be stored in a single Affymetrix Tiling Array. For example, an array could contain probes from Chromosome 21 and Chromosome 22. The sequenceNum uniquely specifies a sequence. Information about this sequence could be determined in this function. The total number of sequences a tiling array contains can be determined in ReadBPMAPHeader(fileName). The sequenceNum indexes from 0 to (total number of sequences -1).

Usage

ReadBPMAPAllSeqHeader(fileName)

Arguments

fileName

the full path of the BPMAP file to be read.

Value

A list of vectors containing SeqName, GroupName, version, npnrobeMapping, seqNum, and NumHits.

Details

The BPMAP Sequence Header gives information about the design of the tiling array.

See Also

BPMAPCelParser() for an one-step BPMAP/CEL parser and affyTile for information about the package.

Examples

####################################################
#The data are in inst/doc folder in rMAT package.
####################################################


pwd<-"" #INPUT FILES- BPMAP, ARRAYS, etc.
path<- system.file("extdata", "Sc03b_MR_v04_10000.bpmap",package="rMAT")

bpmapFile<-paste(pwd,path,sep="")

pathCEL<- system.file("extdata", "Swr1WTIP_Short.CEL",package="rMAT")
arrayFile<-paste(pwd,c(pathCEL),sep="")


# Show the all the different sequences
ReadBPMAPAllSeqHeader(bpmapFile)