priorGenerate: Generate prior for ChIP-seq alignment.

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

Description

priorGenerate generates prior file from ChIP-seq data which will be used in CSEM alignment under --prior option.

Usage

priorGenerate(object, chipFile, maxHistone = 6, outfileLoc = "./")

Arguments

object	The S4 class object generated by priorProcess or priorHistone_multi function.
chipFile	ChIP-seq input files, in fastq format or sam format to save time if it is already aligned and includes multi-mapping reads. If aligned BAM file with multi-mapping reads are ready, readAllocate function can be utilized to tranform the format say into tagAlign or bed.
maxHistone	Maximum number of histone ChIP-seq datasets used in the model. Default value is 6 and we recommend the maximum number of histone ChIP-seq datasets to be under or equal to 6.
outfileLoc	Directory to store processed output files.

Details

This function generates as many prior files as ChIP-seq dataset(s) given as the argument to be used in CSEM software with prior option.

Aligned sam file will go through filtering process to remove duplicates. By default, samtools will be used to remove duplicates. PICARD will be employed if user provide the PICARD jar path.

If the users have already aligned ChIP-seq fastq formatted file, to save time, they can provide the aligned sam formatted file as long as they have included the multi-mapping reads when they did the alignment.

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

Value

A new "Prior" object containing new information which includes:

prior	Location of prior files created.
outfileLoc	Directory where processed files are (given as an argument).
histoneGrpL	Histone data included in the model after variable selection. Provided no histone data, histoneGrpL will not be created.
chipName	Name of ChIP-seq dataset(s).

Author(s)

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

Examples

## Not run: 
object = priorGenerate(object, chipFile, maxHistone, outfileLoc="./")

## End(Not run)

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