BPMAPCelParser: BPMAP and CEL files Reader

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

Description

One-step reading of BPMAP and CEL files, using Fusion SDK and affxparser.

Usage

BPMAPCelParser(BPMAPFileName, CelFileNames, genomeName=NULL, verbose=FALSE,groupName="",seqName="")

Arguments

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

Details

This function returns an object of class tilingSet containing all necessary information: probe sequences, genomic positions, chromosomes as well as the probe intensities.

Value

An object of class tilingSet.

Author(s)

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

See Also

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)

# 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)

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