priorHistone_multi: Process Histone data to cluster positions.

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

Description

Construct required files for generating priors for ChIP-seq data based on only Histone data.

Usage

priorHistone_multi(object, dnaseIndex, outfileLoc="./", outfile = "histoneOnly")

Arguments

object	A "Prior" S4 object generated by priorHistone_init. If not provided, the default value will be NULL.
dnaseIndex	Index of data which will be used as DNase-seq data in the model. Default value will be 1.
outfileLoc	Directory to store processed files. Default is set to "./"
outfile	Infix of outfile name. Default is set to "histoneOnly" to indicate the prior is built by Histone datasets only.

Details

This function processes the Histone files and generates module for further analysis.

Value

A new "Prior" object is created with new information updated:

dnaseName	Name of DNase-seq dataset is the selected histone ChIP-seq dataset used as DNase-seq in the prior construction.
dnaseKnots	DNase knots (from histone ChIP-seq file used as DNase-seq) 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.
dnaseAlign	Aligment information of the DNase file (from histone ChIP-seq file used as DNase-seq) from bowtie.
dataNum	Number of data sets ("DNase-seq" and histone ChIP-seq data sets).
histoneNum	Number of histone ChIP-seq files.
histoneName	Name of histone ChIP-seq files.
histoneAlign	Aligment information of the histone ChIP-seq file(s) from bowtie.

Author(s)

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

Examples

## Not run: 
priorobject = priorHistone_multi(object, dnaseIndex,
outfileLoc = "./", outfile)


## End(Not run)

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