findSummit: Find a summit for each peak region

In dongjunchung/mosaics: MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)

Description

Find a summit for each peak region in the MosaicsPeak class object, which is a peak calling result.

Usage

findSummit( object, ... )
## S4 method for signature 'MosaicsPeak'
findSummit( object, parallel=FALSE, nCore=8 )

Arguments

object	Object of class MosaicsPeak, a peak list object obtained using either functions mosaicsPeak or mosaicsPeakHMM.
parallel	Utilize multiple CPUs for parallel computing using "parallel" package? Possible values are TRUE (utilize multiple CPUs) or FALSE (do not utilize multiple CPUs). Default is FALSE (do not utilize multiple CPUs).
nCore	Number of CPUs when parallel computing is utilized.
...	Other parameters to be passed through to generic findSummit.

Details

Note that extractReads should be run first because findSummit is used.

Value

Construct MosaicsPeak class object.

Author(s)

Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles

References

Kuan, PF, D Chung, G Pan, JA Thomson, R Stewart, and S Keles (2011), "A Statistical Framework for the Analysis of ChIP-Seq Data", Journal of the American Statistical Association, Vol. 106, pp. 891-903.

Chung, D, Zhang Q, and Keles S (2014), "MOSAiCS-HMM: A model-based approach for detecting regions of histone modifications from ChIP-seq data", Datta S and Nettleton D (eds.), Statistical Analysis of Next Generation Sequencing Data, Springer.

See Also

mosaicsPeak, mosaicsPeakHMM, export, extractReads, adjustBoundary, filterPeak, MosaicsPeak.

Examples

## Not run: 
library(mosaicsExample)

constructBins( infile=system.file( file.path("extdata","wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_chr22_sorted.bam"), package="mosaicsExample"), 
    fileFormat="bam", outfileLoc="~/", 
    byChr=FALSE, useChrfile=FALSE, chrfile=NULL, excludeChr=NULL, 
    PET=FALSE, fragLen=200, binSize=200, capping=0 )
constructBins( infile=system.file( file.path("extdata","wgEncodeBroadHistoneGm12878ControlStdAlnRep1_chr22_sorted.bam"), package="mosaicsExample"), 
    fileFormat="bam", outfileLoc="~/", 
    byChr=FALSE, useChrfile=FALSE, chrfile=NULL, excludeChr=NULL, 
    PET=FALSE, fragLen=200, binSize=200, capping=0 )

binHM <- readBins( type=c("chip","input"),
    fileName=c( "~/wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_chr22_sorted.bam_fragL200_bin200.txt",
    "~/wgEncodeBroadHistoneGm12878ControlStdAlnRep1_chr22_sorted.bam_fragL200_bin200.txt" ) )
fitHM <- mosaicsFit( binHM, analysisType="IO", bgEst="rMOM" )
hmmHM <- mosaicsFitHMM( fitHM, signalModel = "2S", 
  init="mosaics", init.FDR = 0.05, parallel=TRUE, nCore=8 )
peakHM <- mosaicsPeakHMM( hmmHM, FDR = 0.05, decoding="posterior",
  thres=10, parallel=TRUE, nCore=8 )

peakHM <- extractReads( peakHM,
  chipFile=system.file( file.path("extdata","wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_chr22_sorted.bam"), package="mosaicsExample"),
  chipFileFormat="bam", chipPET=FALSE, chipFragLen=200,
  controlFile=system.file( file.path("extdata","wgEncodeBroadHistoneGm12878ControlStdAlnRep1_chr22_sorted.bam"), package="mosaicsExample"), 
  controlFileFormat="bam", controlPET=FALSE, controlFragLen=200, parallel=TRUE, nCore=8 )
peakHM <- findSummit( peakHM, parallel=TRUE, nCore=8 )
peakHM <- adjustBoundary( peakHM, parallel=TRUE, nCore=8 )
peakHM <- filterPeak( peakHM, parallel=TRUE, nCore=8 )

export( peakHM, type = "narrowPeak", filename = "./peakHM.narrowPeak" )
export( peakHM, type = "broadPeak", filename = "./peakHM.broadPeak" )

## End(Not run)

dongjunchung/mosaics documentation built on March 1, 2020, 3:44 a.m.