computeMATScore: Detection of enriched regions

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

Description

This function is used to compute the rMAT scores following normalization of expression values in order to locate putative enriched regions. This function is now defunct now defunct and you should instead use 'computeMATScore'.

Usage

 computeMATScore(tilingSet, cName=NULL, dMax=600, verbose=FALSE)
        
 

Arguments

tilingSet	This object contains an ExpressionSet
cName	Unique identifier of control name
dMax	An integer value. The sliding window side of which the adjacent probes are to average upon in order to compute the rMAT score.
verbose	A logical value. If verbose is TRUE, progress information would be displayed.

Details

For more details on the calculation of the rMAT score, pvalues, etc, please refer to the following paper: Johnson et al. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA (2006) vol. 103 (33) pp. 12457-62

Value

The rMAT Score, pValues, and regions. For the regions vector, let 0 denotes the unenriched region. If an enriched region is found, the interval of the region is labeled by a none 0 value. The first region detected is abeled 1 and the next regions are subsequently incremented.

Author(s)

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

See Also

NormalizeProbes, computeMATScore, callEnrichedRegions for normalizing expression values before computing the rMAT enriched regions.

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)

ScSetNorm<-NormalizeProbes(ScSet, method="MAT",robust=FALSE, all=FALSE, standard=TRUE, verbose=FALSE)
	
RD<-computeMATScore(ScSetNorm,cName=NULL, dMax=600, verbose=TRUE) 
	

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