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

In yezhengSTAT/permseq_0.3.0: Mapping protein-DNA interactions in highly repetitive regions of the genomes with prior-enhanced read mapping

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

showClass("Prior")

yezhengSTAT/permseq_0.3.0 documentation built on May 24, 2019, 2:07 a.m.