getCovStats: getCovStats

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

getCovStats

Description

Assembles read distribution statistics from a set of bigwig files based on random windows.

Usage

getCovStats(
  x,
  binSize = 1000,
  nbBins = 10000,
  exclude = NULL,
  canonical.chr = TRUE,
  maxCovQuant = 0.999,
  BPPARAM = SerialParam()
)

Arguments

x	A (named) vector of paths to bigwig files (all from the same genome)
binSize	The size of bins
nbBins	The approximate number of random bins. More bins gives more accurate readouts but take longer to read and compute.
exclude	Region to exclude
canonical.chr	Logical; whether to restrict the sampling to standard chromosomes.
maxCovQuant	The quantile to use as maximum coverage (default 0.999)
BPPARAM	BioParallel BPPARAM for multithreading across files.

Value

A named list of QC tables

Examples

# we use an example bigwig file
bwf <- system.file("extdata/example_atac.bw", package="epiwraps")
# because most of the file is empty, we'll exclude some of the ranges
cs <- getCovStats(bwf, exclude=GRanges("1", IRanges(1, 4300000)))
plotCovStats(cs)

ETHZ-INS/epiwraps documentation built on Dec. 22, 2024, 4:05 a.m.