dpeakRead: Import peak list and aligned read files

In carter-allen/dpeak: dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

Description

Import and process peak list and aligned read files.

Usage

dpeakRead( peakfile=NULL, readfile=NULL, fileFormat="eland_result", 
    PET=FALSE, fragLen=200, parallel=FALSE, nCore=1, tempDir=NULL, perl = "perl" )

Arguments

peakfile	File name of the peak list.
readfile	Name of the aligned read file.
fileFormat	Format of the aligned read file to be processed. For single-end tag (SET) ChIP-seq data, dpeakRead permits the following aligned read file formats: "eland_result" (Eland result), "eland_extended" (Eland extended), "eland_export" (Eland export), "bowtie" (default Bowtie), "sam" (SAM), and "bed" (BED). For paired-end tag (PET) ChIP-seq data, dpeakRead permits only "eland_result" (Eland result format).
PET	Is the aligned read file paired-end tag (PET)? Possible values are either TRUE (PET) or FALSE (SET). Default is FALSE (SET).
fragLen	Average fragment length. Default is 200. Not relevant when PET=TRUE.
parallel	Utilize multiple CPUs for parallel computing using "parallel" package? Possible values are TRUE (use "parallel") or FALSE (not use "parallel"). Default is FALSE (not use "parallel").
nCore	Number of CPUs when parallel computing is utilized.
tempDir	Directory to store temporary files. If tempDir=NULL, dpeakRead() will use the temporary directory used by R.
perl	Name of the perl executable to be called. Default is "perl".

Details

The first three columns of the peak list file (specifed as peakfile) are assumed to be chromosome, start and end positions of each peak region. There should be no header in the peak list file.

When the data contains multiple chromosomes, parallel computing can be utilized for faster preprocessing if parallel=TRUE and parallel package is installed. nCore determines number of CPUs used for parallel computing.

Value

Construct DpeakData class object.

Author(s)

Dongjun Chung

See Also

dpeakFit, DpeakData.

Examples

# PET data

# dataPET <- dpeakRead( peakfile="examplePeak.txt", readfile="examplePETRead.txt", 
#    fileFormat="eland_result", PET=TRUE )

# SET data

# dataSET <- dpeakRead( peakfile="examplePeak.txt", readfile="exampleSETRead.txt", 
#    fileFormat="eland_result", PET=FALSE, fragLen=150 )

data(exampleData)

carter-allen/dpeak documentation built on April 23, 2020, 4:09 p.m.