ReadBPMAPAllSeqHeader: Reading All the BPMAP Sequence Header

In rMAT: R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.

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.

Details

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

Value

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

Author(s)

Charles Cheung, [e-mail] and Raphael Gottardo, [e-mail] Arnaud Droit, [e-mail]

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)

rMAT documentation built on May 6, 2019, 2:10 a.m.