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getCovStats

getCovStats.Rd

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)