plotreg {iSeq} | R Documentation

## A function used to plot enriched genomic regions

### Description

A function used to plot enriched genomic regions.

### Usage

    plotreg(gpos,ipct,conct,peak,col=c("yellow","green","grey0","blue"))

### Arguments

`gpos` | A n by 2 matrix or data frame. The rows correspond to genomic bins. The first and second columns contain the start and end positions of the genomic windows/bins, respectively.
`ipct` | A n by 2 matrix containing the ChIP tag counts corresponding to the bins in gpos. ipct[,1] contains the counts for the chain 1 (usually the forward chain); ipct[,2] contains the counts for the chain 2 (usually the reverse chain).
`conct` | A n by 2 matrix containing the control tag counts corresponding to the bins in gpos. ipct[,1] contains the counts for the chain 1 (usually the forward chain); ipct[,2] contains the counts for the chain 2 (usually the reverse chain).
`peak` | A vector containing the peak (center) positions of the genomic regions.
`col` | The colors used to fill the rectangles. col[1] is used for ipct[,1], col[2] for ipct[,2], col[3] for conct[,1] and col[4] for conct[,2], respectively.

### Value

No value returned.

### Author(s)

Qianxing Mo qianxing.mo@moffitt.org

### References

Qianxing Mo. (2012). A fully Bayesian hidden Ising model for ChIP-seq data analysis. Biostatistics 13(1), 113-28.

### See Also

`iSeq1`, `iSeq2`, `peakreg`,`mergetag`

### Examples

    #see the example in iSeq1

[Package iSeq version 1.44.0 Index]