calculate.pdr.by.chromosome: calculate.pdr.by.chromosome

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

This function calculates the PDR scores for the reads given in the bam files for the CpGs present in the annotation.

Usage

calculate.pdr.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

Value

vector of pdr scores for the given CpG sites in anno

Author(s)

Michael Scherer

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