plotCoverage: utility fn from Patrick Abouyoun's 2010 seminar

Description Usage Arguments Value Examples

View source: R/plotCoverage.R

Description

utility fn from Patrick Abouyoun's 2010 seminar

Usage

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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

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#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.