GRCovFiltration: Exclusion of restriction sites with insufficient coverage

In alekseizarubin/RMetSeq: Restriction Analysis of DNA Methylation

Exclusion of restriction sites with insufficient coverage

Description

Exclusion of restriction sites with insufficient coverage

Usage

GRCovFiltration(
  bamFiles,
  GR,
  tread = 1,
  mincov = 30,
  minSample = 1,
  duplicate = T
)

Arguments

bamFiles	Vector with bam file names
GR	GRanges object with coordinates of restriction sites
tread	The number of running threads at the same time, doesn't work in windows.
mincov	Minimum coverage.
minSample	Minimum number of samples for which the restriction site has the minimum amount of coverage.
duplicate	Remove duplicates

Value

Filtered Granges object

alekseizarubin/RMetSeq documentation built on May 27, 2023, 12:09 p.m.