plotPeak {DBChIP} | R Documentation

## Plot peak

### Description

Plot the coverage profile of differentially bound peaks

### Usage

    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`

[Package DBChIP version 1.24.0 Index]