findSummit {mosaics} | R Documentation |
Find a summit for each peak region in the MosaicsPeak
class object, which is a peak calling result.
findSummit( object, ... ) ## S4 method for signature 'MosaicsPeak' findSummit( object, parallel=FALSE, nCore=8 )
object |
Object of class |
parallel |
Utilize multiple CPUs for parallel computing
using |
nCore |
Number of CPUs when parallel computing is utilized. |
... |
Other parameters to be passed through to generic |
Note that extractReads
should be run first because findSummit
is used.
Construct MosaicsPeak
class object.
Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles
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.
mosaicsPeak
, mosaicsPeakHMM
, export
,
extractReads
, adjustBoundary
, filterPeak
,
MosaicsPeak
.
## 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)