plotCoverage: utility fn from Patrick Abouyoun's 2010 seminar

In biobenkj/ATACseeker: Utilities for ATACseq QC, differential accessibility, and integration

Description

utility fn from Patrick Abouyoun's 2010 seminar

Usage

plotCoverage(x, gr, col = "violet", xlab = "base", ylab = "reads",
  main = "Coverage", stranded = FALSE, smoothen = 0, kf = "normal", ...)

Arguments

x	a galp
gr	a single GRanges range (i.e. seqname, start, end)
col	what color to plot it
xlab	x axis label for the plot
ylab	y axis label for the plot
main	main title for the plot
stranded	plot stranded? (FALSE)
smoothen	smooth the counts? (FALSE)
kf	kernel function for smoothing (normal)
...	arguments to pass along to coverage()

Value

invisibly return coverage and plot

Examples

#visualizing a specific enhancer:
library(GenomicRanges)
library(Mus.musculus)

SMOenh <- GRanges('chr6', IRanges(29744702, 29751934), '+')
seqinfo(SMOenh) <- seqinfo(Mus.musculus)[seqlevels(SMOenh)]

plotCoverage(galp, SMOenh)
plotCoverage(galp, SMOenh, stranded=TRUE)
plotCoverage(get5primeCuts(galp), SMOenh, stranded=TRUE)
plotCoverage(get5primeCuts(galp, shrink=FALSE), SMOenh, stranded=TRUE)

biobenkj/ATACseeker documentation built on May 7, 2019, 8:36 a.m.