plotPeak: Plot peak

Description Usage Arguments See Also

View source: R/DBChIP.R

Description

Plot the coverage profile of differentially bound peaks

Usage

1
plotPeak(rept, dat, lib.size = NULL, w = 400, ext = 200, combine.rep = FALSE, cap = NULL, n.row.per.page = 6, caption = NULL)

Arguments

rept

a data.frame as the result of report.peak.

dat

a list with the following items: chip.list, input.list, matching.input.names, norm.factor.vec. Description of the items can be found in the return value of DBChIP.

lib.size

a vector of library size of each ChIP sample. Used to scale profiles so that they are comparable.

w

half window size to plot around the binding sites.

ext

extension size for each read. Each read is extended from its 5' end by ext towards 3' end. If ext is set to 1, the minimum, per nucleotide read counts will be plotted.

combine.rep

logical, whether to combine replicates for the plot. Can be useful when there are too many replicates to plot.

cap

the maximum number of reads per nucleotide allowd to plot.

n.row.per.page

the maximum number of tracks (rows) per page.

caption

additional caption to appear on the title besides the location.

See Also

DBChIP


DBChIP documentation built on May 2, 2018, 2:46 a.m.