readAllocate: Allocate ChIP-seq reads

In yzheng74/permseq: Mapping protein-DNA interactions in highly repetitive regions of the genomes with prior-enhanced read mapping

Description

Allocate ChIP-Seq multi-reads using prior information.

Usage

readAllocate(object, outfileLoc = "./", outputFormat, outputFilter, chipThres, chipFile,
bowtieDir, bowtieIndex, vBowtie = 2, mBowtie = 99, pBowtie = 8, bwaDir,
bwaIndex, nBWA = 2, oBWA = 1, tBWA = 8, mBWA = 99, csemDir, picardDir, fragL = 200)

Arguments

object	Default set as NULL. A "Prior" S4 object generated by priorGenerate. If object=NULL, then extra parameters, which are chipFile, bowtieIndex, bowtieDir, vBowtie, mBowtie, pBowtie (or bwaDir, bwaIndex, nBWA, oBWA, tBWA, mBWA), csemDir, fragL, need to be defined and CSEM will allocate-multi reads without using prior information (see details for more information).
outfileLoc	Directory to store processed files. Default set as "./".
outputFormat	Output Format. Default is NULL and will only return results in bam format. Possible values are tagAlign and bed
outputFilter	Boolean parameter indicating whether or not the aligned BAM file should be filtered by removing duplicates. If chipThres parameter is also provided, the aligned BAM file will also get rid of low quality scored alignments. Default value is TRUE.
chipThres	For thresholding reads. Default value is NULL and it will not filter the alignment results if users do not specify the threshold. It will select reads with scores higher than chipThres (allocation probability*1000). Default set at NULL and will not threshold reads.
chipFile	Default set as NULL, only needed when object = NULL. ChIP-Seq files, in fastq format or sam format to save time if it is already aligned and includes multi-mapping reads. Aligned BAM format is also accepted for further filtering or format transformation.
bowtieDir	Default set as NULL, only needed when object = NULL. Directory where Bowtie was installed
bowtieIndex	Default set as NULL, only needed when object=NULL. Bowtie index, used in bowtie aligning. Users can specify the aligner, Bowtie or BWA, by specifying the index that will be used.

w

vBowtie	Default set as 2, only needed when object = NULL. Bowtie parameter. In -v mode, alignments may have no more than vBowtie mismatches, where v may be a number from 0 through 3 set using the -v option. Default value is 2.
mBowtie	Default set as 99, only needed when object = NULL. Bowtie parameter. -m parameter instructs bowtie to refrain from reporting any alignments for reads having more than mBowtie reportable alignments. Default value is 99 allowing multi-reads alignment.
pBowtie	Default set as 8, only needed when object = NULL. The -p option causes Bowtie to launch a specified number of parallel search threads. Each thread runs on a different processor/core and all threads find alignments in parallel. Default value is 8.
bwaDir	Default set as NULL, only needed when object = NULL. Directory where BWA was installed.
bwaIndex	Default set as NULL, only needed when object = NULL. BWA index used in BWA alignment. Users can specify the aligner, Bowtie or BWA, by specifying the index that will be used.
nBWA	Default set as 2, only needed when object = NULL. BWA paramter. In "bwa aln -n" mode, if it is an integer, it denotes the maximum edit distances including mismatch and gap open. Otherwise, it will be the fraction of missing alignments given 2% uniform base errr rate.
oBWA	Default set as 1, only neede when object = Null. BWA parameter. In "bwa aln -o" mode, it specifies the maximum number of gap open.
tBWA	Default set as 8, only needed when object = NULL. BWA parameter. In "bwa aln -t" mode, it is the number of threads in multi-threading mode.
mBWA	Default set as 99, only needed when object = NULL. BWA parameter. In "bwa samse -n", it restricts the maximum number of alignments to output for each read. If a read has more hits, the XA tag will not be written.
csemDir	Default set as NULL, only needed when object = NULL. Directory where CSEM was installed.
picardDir	Default set as NULL, the path to the picard jar (jar folder name included) is needed when aligned BAM file need filtering and users want to use picard to remove the duplicates. Otherwise, filtering can be done by samtools if csemDir is provided. If both csemDir and picardDir are provided, picard will be used.
fragL	Default set as 200, only needed when object = NULL. Fragment length.

Details

By default, it will allocate multi-reads using prior information from the object generated by
priorGenerate.

If prior information is not available (DNase and/or histone), do not run priorProcess and priorGenerate. Instead, set object as NULL and give the extra parameters: chipFile, bowtieDir, bowtieIndex, vBowtie, mBowtie, pBowtie, bwaDir, bwaIndex, nBWA, oBWA, tBWA, mBWA, csemDir, and fragL. CSEM will allocate the ChIP-seq.

Users can select from Bowtie and BWA to do the alignment by providing the corresponding index and leaving the other as default value NULL. If both indices are provided, the package will automatically use Bowtie to do the multi-mapping reads alignment.

plot(), summary(), names() and print() methods included. To obtain the alignment information from bowtie use summary().

Value

An updated "Prior" object is returned together with the aligned ChIP-seq output files.

chipSAM	Location of aligned ChIP-seq files in SAM format.
chipAllocate	Location of allocated ChIP-seq files in bam format.
chipFormat	Location of allocated ChIP-seq files in other format (tagAlign or bed).
outfileLoc	Directory where processed files are (given as an argument).

Or if no prior is built and allocate ChIP-seq by CSEM directly, a new "Prior" object will be created.

chipName	Name of ChIP-seq dataset(s).
chipNum	Number of ChIP-seq dataset(s).
chipAlign	ChIP-seq alignment summary feedback from bowtie.
chipSAM	Location of aligned ChIP-seq in SAM format.
chipAllocate	Location of the final allocated ChIP-seq output by Permseq in BAM format.
chipAlignFormat	Location of the final allocated ChIP-seq output by Permseq in other selected format (tagAlign or bed).
chrList	Chromsome list.
fragL	Fragment length.
bowtieInfo	List of bowtie information used: bowtieIndex, bowtieDir, vBowtie, mBowtie and pBowtie.
bwaInfo	List of BWA realted information: bwaDir, bwaIndex, nBWA, oBWA, tBWA, mBWA.
csemDir	Directory where CSEM was installed.
picardDir	Directory where PICARD jar file is saved.
outfileLoc	Directory to store output files.

Author(s)

Xin Zeng, M. Constanza Rojo-Alfaro, Ye Zheng.

Examples

## Not run: 
readAllocate(object, outfileLoc = "./", outputFormat = "tagAligne")

## End(Not run)

yzheng74/permseq documentation built on May 4, 2019, 8:47 p.m.