extractReads: Load read-level data and extract reads corresponding to each...

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

Description

Load read-level data and extract reads corresponding to each peak region in the MosaicsPeak class object, which is a peak calling result.

Usage

extractReads( object, ... )
## S4 method for signature 'MosaicsPeak'
extractReads( object, chipFile=NULL, chipFileFormat=NULL,
    chipPET=FALSE, chipFragLen=200,
    controlFile=NULL, controlFileFormat=NULL, 
    controlPET=FALSE, controlFragLen=200, keepReads=FALSE,
    parallel=FALSE, nCore=8, tempDir=NULL, perl="perl" )

Arguments

object	Object of class MosaicsPeak, a peak list object obtained using either functions mosaicsPeak or mosaicsPeakHMM.
chipFile	Name of the aligned read file for ChIP sample.
chipFileFormat	Format of the aligned read file for ChIP sample. Currently, constructBins permits the following aligned read file formats for SET data (chipPET = FALSE): "eland_result" (Eland result), "eland_extended" (Eland extended), "eland_export" (Eland export), "bowtie" (default Bowtie), "sam" (SAM), "bam" (BAM), "bed" (BED), and "csem" (CSEM). For PET data (chipPET = TRUE), the following aligned read file formats are allowed: "eland_result" (Eland result), "sam" (SAM), and "bam" (BAM).
chipPET	Is the file of ChIP sample paired-end tag (PET) data? If chipPET=FALSE, it is assumed that the file is SET data. If chipPET=TRUE, it is assumed that the file is PET data. Default is FALSE (SET data).
chipFragLen	Average fragment length of ChIP sample. Default is 200. This argument is ignored if chipPET=TRUE.
controlFile	Name of the aligned read file for matched control sample.
controlFileFormat	Format of the aligned read file for matched control sample. Currently, constructBins permits the following aligned read file formats for SET data (controlPET = FALSE): "eland_result" (Eland result), "eland_extended" (Eland extended), "eland_export" (Eland export), "bowtie" (default Bowtie), "sam" (SAM), "bam" (BAM), "bed" (BED), and "csem" (CSEM). For PET data (controlPET = TRUE), the following aligned read file formats are allowed: "eland_result" (Eland result), "sam" (SAM), and "bam" (BAM).
controlPET	Is the file of matched control sample paired-end tag (PET) data? If controlPET=FALSE, it is assumed that the file is SET data. If controlPET=TRUE, it is assumed that the file is PET data. Default is FALSE (SET data).
controlFragLen	Average fragment length of matched control sample. Default is 200. This argument is ignored if controlPET=TRUE.
keepReads	Keep read-level data? Default is FALSE (do not keep read-level data).
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.
tempDir	Directory to store temporary files. If tempDir=NULL, extractReads() will use the temporary directory used by R.
perl	Name of the perl executable to be called. Default is "perl".
...	Other parameters to be passed through to generic extractReads.

Details

Read-level data is first loaded from aligned read files, and then the reads corresponding to each peak region are extracted and incorporated into the MosaicsPeak class object. extractReads currently supports the following aligned read file formats for SET data (chipPET = FALSE and controlPET = FALSE): Eland result ("eland_result"), Eland extended ("eland_extended"), Eland export ("eland_export"), default Bowtie ("bowtie"), SAM ("sam"), BAM ("bam"), BED ("bed"), and CSEM ("csem"). For PET data (chipPET = FALSE and controlPET = FALSE), the following aligned read file formats are allowed: "eland_result" (Eland result), "sam" (SAM), and "bam" (BAM).

If input file format is neither BED nor CSEM BED, this method retains only reads mapping uniquely to the reference genome.

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, findSummit, 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 )

## End(Not run)

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