priorClass: An S4 "Prior" class containing prior information for the...

Description Arguments Author(s) Examples

Description

Methods included in "Prior" class: names(), plot(), print(), summary() and show().

Arguments

dnaseName

Names of datasets that are used as DNase-seq, especially in the "only Histone" situation, dnaseName is the selected histone ChIP-seq dataset.

dnaseAlign

DNase-seq alignment summary information from bowtie.

dnaseKnots

A vector of knots points for the 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.

posLoc_bychr

Location of the files containing the group index of each segment of the genome.

dnaseHistone

The input histone ChIP-seq files which are the candidates for the DNase-seq while running priorProcess procedure.

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 ChIP-seq dataset(s).

histoneAlign

Histone alignment summary information from bowtie.

histoneGrpL

Histone dataset(s) selected to be included in the model after variable selection.

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.

chipAllocate

Location of the final allocated ChIP-seq output by Permseq in BAM format.

chipUni

Location of the aligned ChIP-seq uni-reads files in BED format.

chipFormat

Location of the final allocated ChIP-seq output by Permseq in other selected format (tagAlign or bed).

dataNum

The number of dataset(s) that are used.

chrList

Chromosome list.

fragL

Fragment length.

bowtieInfo

Bowtie information. Includes: location of bowtie index, directory where the bowtie is installled, bowtie parameters values -v, -m and -p.

bwaInfo

BWA related information. Includes: location of bwa index, directory where the BWA is installed, BWA parameters values for "bwa aln -n -o -t" and "bwa samse -n".

csemDir

Directory where CSEM was installed.

picardDir

Directory where PICARD jar file is saved.

outfileLoc

Directory to store output files.

prior

Location where the prior files are saved.

chrom.ref

Name of the file for chromosome info. In this file, the first and second columns are ID and size of each chromosome, respectively.

Author(s)

Ye Zheng, M. Constanza Rojo-Alfaro.

Examples

1
showClass("Prior")

yezhengSTAT/permseq_0.3.0 documentation built on Aug. 17, 2017, 1:27 a.m.