BPMAPCelParser {rMAT} | R Documentation |
One-step reading of BPMAP and CEL files, using Fusion SDK and affxparser.
BPMAPCelParser(BPMAPFileName, CelFileNames, genomeName=NULL, verbose=FALSE,groupName="",seqName="")
BPMAPFileName |
String containing the full filename of the BPMAP file. |
CelFileNames |
Vector of strings containing full filenames of CEL files. i.e. c("F1.CEL", "F2.CEL" |
genomeName |
String containing the genome name used. |
groupName |
String containing the group of genome name used. |
seqName |
String containing the group of sequence name (e.g. chromosome) used. |
verbose |
If verbose is selected, the progress and additional information will be displayed while the function is running |
This function returns an object of class tilingSet
containing all necessary information: probe sequences, genomic positions, chromosomes as well as the probe intensities.
An object of class tilingSet
.
Charles Cheung, cykc@interchange.ubc.ca and Raphael Gottardo, raphael.gottardo@ircm.qc.ca Arnaud Droit, arnaud.droit@ircm.qc.ca
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) # create a tiling Set from the corresponding data # This will only grep the sequences with Sc ScSet<-BPMAPCelParser(bpmapFile, arrayFile, verbose=FALSE,groupName="Sc") # show the object show(ScSet) # summarize its content summary(ScSet)