calculate.pdr: calculate.pdr

Description Usage Arguments Value Author(s)

View source: R/calculate_scores.R

Description

This function calculates the PDRs for all analyzed CpG sites in the bam file of the corresponding sample

Usage

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calculate.pdr(
  bam.file,
  anno,
  log.path = getwd(),
  cores = 1,
  window.size = unname(get.option("window.size")),
  max.reads = unname(get.option("max.reads")),
  mapq.filter = unname(get.option("mapq.filter")),
  coverage.threshold = unname(get.option("coverage.threshold")),
  use.sex.chromosomes = FALSE,
  ignore.strand = TRUE
)

Arguments

bam.file

bath to the bam file to be analyzed already aligned to a reference genome

anno

annotation as a GRanges object with the CpG sites to be analyzed

log.path

location of the log file

cores

number of cores available for the analysis

use.sex.chromosomes

Flag indicating if scores are also to be computed for the sex chromosomes

ignore.strand

The ignore.strand parameter from the function findOverlaps

Value

PDR scores for the given annotation.

Author(s)

Michael Scherer


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