priorHistone_init: Process histone ChIP-seq dataset to build the prior without...

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

Description

If no DNase-seq dataset available, process Histone data and select the histone ChIP-seq dataset who shows the strongest relationship with ChIP-seq data. The selected histone ChIP-seq data will be used as DNase-seq data in the model.

Usage

priorHistone_init(histoneFile = NULL, histoneName = NULL, chipFile = NULL, fragL = 200,
AllocThres = 900, chrList, capping = 0, outfileLoc = "./", 
bowtieDir, bowtieIndex, vBowtie = 2, mBowtie = 99,
pBowtie = 8, bwaDir, bwaIndex, nBWA = 2, oBWA = 1, tBWA = 8, mBWA = 99,
csemDir, picardDir, saveFiles = TRUE)

Arguments

histoneFile	Input histone ChIP-seq file in fastq format. For faster results, sam formatted file after alignment including multi-mapping reads or bam or bed files already obtained by CSEM with allocated reads can also be processed, if available. Otherwise, it is better start from the fastq formatted file. Default value is NULL.
histoneName	Name of the histone ChIP-seq data. If multiple Histone data are used, it needs to be formed into a vector.
chipFile	Input ChIP-seq files, in fastq format or sam format to save time if it is already aligned and includes multi-mapping reads. The default value will be NULL.
fragL	Average fragment length. The default value is 200.
AllocThres	Allocation threshold. It will select reads with scores higher than AllocThres (allocation probability*1000). Default set at 900.
chrList	A vector of chromosomes that will be included in the analysis. Default set as NULL and priorHistone_init will get the list from processed files. Otherwise, if given by the user, it should be consistent with the chromosome name(s) in the corresponding fasta file(s). For more information, see details.
capping	Maximum number of reads allowed to start at each nucleotide position. To avoid potential PCR amplification artifacts, the maximum number of reads that can start at a nucleotide position is capped. Default is 0 (no capping, i.e. no maximum restriction).
outfileLoc	Directory to store processed files. Default is set to "./".
bowtieDir	Directory where Bowtie was installed. Default will be NULL.
bowtieIndex	Bowtie index, used in bowtie alignment. Users can select the aligner, Bowtie or BWA, by providing the corresponding index. Default will be NULL.
vBowtie	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	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 all kinds of multi-reads alignment.
pBowtie	Bowtie parameter. 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 paralle. Default value is 8.
bwaDir	Directory where BWA was installed. Default set as NULL.
bwaIndex	BWA index used in BWA alignment. Users can specify the aligner, Bowtie or BWA, by specifying the index that will be used. Default set as NULL.
nBWA	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. Default value is 2.
oBWA	BWA parameter. In "bwa aln -o" mode, it specifies the maximum number of gap open. Default set as 1.
tBWA	BWA parameter. In "bwa aln -t" mode, it is the number of threads in multi-threading mode. Default set as 8.
mBWA	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. Default set as 99.
csemDir	Directory where CSEM was installed. The default value is NULL.
picardDir	Directory where PICARD jar file is saved.
saveFiles	Option to save intermediate files created. Default set as TRUE.

Details

Process histone ChIP-seq files and generate module for further analysis in
priorHistone_multi.

This function processes the histone ChIP-seq files and generates a marginal plot (marginal_plot.pdf) stored in outfileLoc to decide which histone data should be used as DNase-seq data (choose the histone ChIP-seq data which has the most increasing relationship with ChIP data).

If no chrList is provided, priorHistone_init will generate the list from processed files (.sam file if Histone input file is in fastq format or .bed file if Histone input file is in .bam or .bed format). Otherwise, if given by the user, it will accelerate the procedure, but the chrList should be consistent with the chromosome name(s) in the corresponding .fa or .fasta file(s). In other words, for example, it should be the name on the first line after ">" in .fa file.

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.

Aligned sam file will go through filtering process to remove duplicates. By default, 'samtools rmdup -s' will be used to carry out such function. If user provides the PICARD jar path, PICARD will be used.

plot(), summary(), names() and print() methods can be used to see the information contained in "Prior" object. To obtain the ChIP-seq (or Histone) alignment information from bowtie, use summary().

Value

A new "Prior" object is created.

First, for each histone ChIP-seq dataset within dnaseHistone

dnaseKnots	Knots for B-spline functions. They are the 90, 99 and 99.9th percentiles of read counts.
dnaseThres	A vector of DNase-seq group created to generate aggregated ChIP data. After alignment, positions which have the same DNase-seq read count are clustered into one group. dnaseThres is the corresponding read count number in each group. Each count is corresponding to one group and the grouping data partitions the whole genome into multiple segments.
posLoc_bychr	Location of the files containing the group index of each segment of the genome.
posLoc3_bychr	Location of the files containing which segments of the genome are in which group based on the trinary Histone positions according to 90 and 99th percentiles of read counts.

Other elements of the "Prior" include:

chipName	Name of ChIP-seq dataset(s).
chipNum	Number of ChIP-seq dataset(s).
chipAlign	ChIP-seq alignment summary information from bowtie.
chipSAM	Location of aligned ChIP-seq in SAM format.
chipUni	Location of the aligned ChIP-seq uni-reads files in BED format.
histoneName	Name of histone ChIP-seq dataset(s). If no giving values, histoneName is set as a vector of index number(1:length(histoneFile)).
histoneNum	Number of Histone dataset(s).
histoneAlign	Histone alignment summary information from bowtie.
chrList	Chromosome list.
fragL	Fragment length, given as a parameter.
bowtieInfo	List of bowtie information used: bowtieIndex, bowtieDir, vBowtie, mBowtie and pBowtie.
bwaInfo	List of BWA related information: bwaDir, bwaIndex, nBWA, oBWA, tBWA, mBWA.
csemDir	Directory of CSEM given as a parameter.
picardDir	Directory where PICARD jar file is saved.
chrom.ref	Name of the file for chromosome info, given as a parameter.
outfileLoc	Directory where processed files are (given as an argument).

Author(s)

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

Examples

## Not run: 
object = priorHistone_init(histoneFile = NULL, histoneName = NULL,
  chipFile, fragL, AllocThres = 900, chrList, capping = 0, outfileLoc = "./",
  bowtieDir,  bowtieIndex,  vBowtie = 2,
  mBowtie = 99, pBowtie = 8, csemDir, picardDir, saveFiles = TRUE)

## End(Not run)

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