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

Description Usage Arguments Details Value Author(s)

View source: R/calculate_scores.R

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

1
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/WSH_package documentation built on Oct. 19, 2021, 12:14 p.m.