calculate.fdrp.score: calculate.fdrp.score

Description Usage Arguments Value Author(s)

View source: R/calculate_scores.R

Description

This function calculates the FDRPs/qFDRPs (depending on how the options are set) for all CpG sites in the annotation from the reads provided by the bam file.

Usage

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calculate.fdrp.score(
  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

CpG sites to be analyzed as a GRanges object

log.path

location of the log file

cores

number of cores available for the analysis

window.size

window size used to restrict the concordance/discordance classification of each read pair DEFAULT: 50 as the maximum distance

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

FDRP scores for the given annotation.

Author(s)

Michael Scherer


MPIIComputationalEpigenetics/WSHPackage documentation built on Oct. 22, 2021, 2:07 p.m.