ReadBPMAPAllSeqHeader {rMAT} | R Documentation |
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).
ReadBPMAPAllSeqHeader(fileName)
fileName |
the full path of the BPMAP file to be read. |
The BPMAP Sequence Header gives information about the design of the tiling array.
A list of vectors containing SeqName, GroupName, version, npnrobeMapping, seqNum, and NumHits.
Charles Cheung, cykc@interchange.ubc.ca and Raphael Gottardo, raphael.gottardo@ircm.qc.ca Arnaud Droit, arnaud.droit@ircm.qc.ca
BPMAPCelParser()
for an one-step BPMAP/CEL parser and affyTile
for information about the package.
#################################################### #The data are in inst/doc folder in rMAT package. #################################################### pwd<-"" #INPUT FILES- BPMAP, ARRAYS, etc. path<- system.file("doc/Sc03b_MR_v04_10000.bpmap",package="rMAT") bpmapFile<-paste(pwd,path,sep="") pathCEL<- system.file("doc/Swr1WTIP_Short.CEL",package="rMAT") arrayFile<-paste(pwd,c(pathCEL),sep="") # Show the all the different sequences ReadBPMAPAllSeqHeader(bpmapFile)