plot_cher: Plot identified Chers

In Ringo: R Investigation of ChIP-chip Oligoarrays

Description

Function for plotting identified Chers (ChIP-enriched regions).

Usage

## S4 method for signature 'cher,ExpressionSet'
plot(x, y, probeAnno, samples=NULL, extent = 1000, gff = NULL, ...)

Arguments

x	object of class cher
y	data object of class ExpressionSet that was used for function findChersOnSmoothed
probeAnno	object of class probeAnno holding the reporter/probe to genome mappings
samples	which samples to plot, either a numeric vector of entries in 1 to ncol(dat), or character vector with entries in sampleNames(dat) or NULL meaning plot the levels from all samples in the ExpressionSet
extent	integer; how many base pairs to the left and right should the plotted genomic region be extended
gff	data frame with gene/transcript annotation
...	further arguments passed on to function chipAlongChrom

Value

called for generating the plot; invisible(NULL)

Author(s)

Joern Toedling

See Also

chipAlongChrom, cher-class

Ringo documentation built on Nov. 8, 2020, 5:34 p.m.