calculate.fdrp.by.chromosome: calculate.fdrp.by.chromosome This function calculates the...

In MPIIComputationalEpigenetics/WSHPackage: R package for the calculation of the following Within-Sample Heterogeneity Scores in Bisulfite Sequencing Data: FDRP, qFDRP, PDR, Epipolymorphism, Methylation Entropy and MHL

Description

calculate.fdrp.by.chromosome This function calculates the FDRP scores for the reads given in the bam files for the CpGs present in the annotation.

Usage

calculate.fdrp.by.chromosome(bam, anno, ignore.strand = TRUE)

Arguments

bam	bam file with the reads from a bisulfite sequencing technique already aligned to a reference genome
anno	annotation as a GRanges object with the CpG sites to be analyzed
ignore.strand	The ignore.strand parameter from the function findOverlaps

Details

This function is called by calculate.fdrps for each chromosome separately and calls toCpG as well as calculate.fdrp.site.

Value

vector of fdrp scores for the given CpG sites in anno

Author(s)

Michael Scherer

MPIIComputationalEpigenetics/WSHPackage documentation built on Dec. 14, 2021, 11:49 a.m.