mosaics-package {mosaics} | R Documentation

## MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)

### Description

This package provides functions for fitting MOSAiCS, a statistical framework to analyze one-sample or two-sample ChIP-seq data.

### Details

Package: | mosaics
Type: | Package
Version: | 2.9.9
Date: | 2016-03-15
License: | GPL (>= 2)
LazyLoad: | yes

This package contains four main classes, `BinData`, `MosaicsFit`, `MosaicsHMM`, and `MosaicsPeak`, which represent bin-level ChIP-seq data, MOSAiCS model fit, MOSAiCS-HMM model fit, and MOSAiCS peak calling results, respectively. This package contains ten main methods, `constructBins`, `readBins`, `mosaicsFit`, `mosaicsPeak`, `mosaicsFitHMM`, `mosaicsPeakHMM`, `extractReads`, `findSummit`, `adjustBoundary`, `filterPeak`. `constructBins` method constructs bin-level files from the aligned read file. `readBins` method imports bin-level data and construct `BinData` class object. `mosaicsFit` method fits a MOSAiCS model using `BinData` class object and constructs `MosaicsFit` class object. `mosaicsPeak` method calls peaks using `MosaicsFit` class object and construct `MosaicsPeak` class object. `mosaicsFitHMM` and `mosaicsPeakHMM` are designed to identify broad peaks and their functions correspond to `mosaicsFit` and `mosaicsPeak`, respectively. `mosaicsFitHMM` method fits a MOSAiCS-HMM model using `MosaicsFit` class object and constructs `MosaicsHMM` class object. `mosaicsPeakHMM` method calls MOSAiCS-HMM peaks using `MosaicsHMM` class object and construct `MosaicsPeak` class object. `extractReads`, `findSummit`, `adjustBoundary`, `filterPeak` methods postprocess MOSAiCS and MOSAiCS-HMM peaks using `MosaicsPeak` class object (incorporate read-level data, identify peak summits, adjust peak boundaries, and filter potential false positive peaks, respectively) and construct `MosaicsPeak` class object. `MosaicsPeak` class object can be exported as text files or transformed into data frame, which can be used for the downstream analysis. This package also provides methods for simple exploratory analysis.

The `mosaics` package companion website, http://www.stat.wisc.edu/~keles/Software/mosaics/, provides preprocessing scripts, preprocessed files for diverse reference genomes, and easy-to-follow instructions. We encourage questions or requests regarding `mosaics` package to be posted on our Google group, http://groups.google.com/group/mosaics_user_group. Please check the vignette for further details on the `mosaics` package and these websites.

### Author(s)

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

Maintainer: Dongjun Chung <dongjun.chung@gmail.com>

### 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

`constructBins`, `readBins`, `mosaicsFit`, `mosaicsPeak`, `mosaicsFitHMM`, `mosaicsPeakHMM`, `extractReads`, `findSummit`, `adjustBoundary`, `filterPeak`, `BinData`, `MosaicsFit`, `MosaicsHMM`, `MosaicsPeak`.

### Examples

    ## Not run:
    library(mosaicsExample)

    # example analysis workflow for ChIP-seq data of transcription factor binding
    # (STAT1 factor binding in GM12878 cell line, from ENCODE database)

    generateWig( infile=system.file( file.path("extdata","wgEncodeSydhTfbsGm12878Stat1StdAlnRep1_chr22_sorted.bam"), package="mosaicsExample"),
        fileFormat="bam", outfileLoc="./",
        PET=FALSE, fragLen=200, span=200, capping=0, normConst=1 )

    constructBins( infile=system.file( file.path("extdata","wgEncodeSydhTfbsGm12878Stat1StdAlnRep1_chr22_sorted.bam"), package="mosaicsExample"),
        fileFormat="bam", outfileLoc="./",
        PET=FALSE, fragLen=200, binSize=200, capping=0 )
    constructBins( infile=system.file( file.path("extdata","wgEncodeSydhTfbsGm12878InputStdAlnRep1_chr22_sorted.bam"), package="mosaicsExample"),
        fileFormat="bam", outfileLoc="./",
        PET=FALSE, fragLen=200, binSize=200, capping=0 )

    binTFBS <- readBins( type=c("chip","input"),
        fileName=c( "./wgEncodeSydhTfbsGm12878Stat1StdAlnRep1_chr22_sorted.bam_fragL200_bin200.txt",
        "./wgEncodeSydhTfbsGm12878InputStdAlnRep1_chr22_sorted.bam_fragL200_bin200.txt" ) )
    binTFBS
    head(print(binTFBS))
    plot(binTFBS)
    plot( binTFBS, plotType="input" )

    fitTFBS <- mosaicsFit( binTFBS, analysisType="IO", bgEst="rMOM" )
    fitTFBS
    plot(fitTFBS)

    peakTFBS <- mosaicsPeak( fitTFBS, signalModel="2S", FDR=0.05,
    maxgap=200, minsize=50, thres=10 )
    peakTFBS
    head(print(peakTFBS))

    peakTFBS <- extractReads( peakTFBS,
      chipFile=system.file( file.path("extdata","wgEncodeSydhTfbsGm12878Stat1StdAlnRep1_chr22_sorted.bam"), package="mosaicsExample"),
      chipFileFormat="bam", chipPET=FALSE, chipFragLen=200,
      controlFile=system.file( file.path("extdata","wgEncodeSydhTfbsGm12878InputStdAlnRep1_chr22_sorted.bam"), package="mosaicsExample"),
      controlFileFormat="bam", controlPET=FALSE, controlFragLen=200, parallel=TRUE, nCore=8 )
    peakTFBS

    peakTFBS <- findSummit( peakTFBS, parallel=FALSE, nCore=8 )

    export( peakTFBS, type = "txt", filename = "./peakTFBS.txt" )
    export( peakTFBS, type = "bed", filename = "./peakTFBS.bed" )
    export( peakTFBS, type = "gff", filename = "./peakTFBS.gff" )
    export( peakTFBS, type = "narrowPeak", filename = "./peakTFBS.narrowPeak" )

    # example analysis workflow for ChIP-seq data of histone modification
    # (H3K4me3 modification in GM12878 cell line, from ENCODE database)

    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 )

    fileName <- file.path(
        c("wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_chr22_sorted.bam_fragL200_bin200.txt",
          "wgEncodeBroadHistoneGm12878ControlStdAlnRep1_chr22_sorted.bam_fragL200_bin200.txt"))
    binHM <- readBins( type=c("chip","input"), fileName=fileName )
    binHM
    plot(binHM)
    plot( binHM, plotType="input" )

    fitHM <- mosaicsFit( binHM, analysisType="IO", bgEst="rMOM" )
    fitHM
    plot(fitHM)

    hmmHM <- mosaicsFitHMM( fitHM, signalModel = "2S",
      init="mosaics", init.FDR = 0.05, parallel=TRUE, nCore=8 )
    hmmHM
    plot(hmmHM)

    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

    peakHM <- findSummit( peakHM, parallel=TRUE, nCore=8 )
    head(print(peakHM))
    plot( peakHM, filename="./peakplot_HM.pdf" )

    peakHM <- adjustBoundary( peakHM, parallel=TRUE, nCore=8 )
    peakHM
    head(print(peakHM))

    peakHM <- filterPeak( peakHM, parallel=TRUE, nCore=8 )
    peakHM
    head(print(peakHM))

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

    ## End(Not run)

[Package mosaics version 2.25.0 Index]