coverage.plot.raw: Plot the raw coverage in a region

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

Description

Plot the raw read coverage in a genomic regions across samples.

Usage

coverage.plot.raw(chr, start, end, files.df, samples, proper = TRUE,
  map.quality = 30, bp.res = 1, flanks = NULL)

Arguments

chr	chromosome
start	genomic coordinate
end	genomic coordinate
files.df	a data.frame with the path to the bam files
samples	the samples to represent
proper	should proper mapping be counted. Default is TRUE.
map.quality	the minimum mapping quality. Default is 30.
bp.res	the resolution, in bp. Default is 1 bp.
flanks	the amount of bp to add in the flanks.

Value

a ggplot object

Author(s)

Jean Monlong

jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.