metaGene {groHMM} | R Documentation

## Returns a histogram of the number of reads in each section of a moving window centered on a certain feature.

### Description

Supports parallel processing using mclapply in the 'parallel' package. To change the number of processors, set the option 'mc.cores'.

### Usage

    metaGene(features, reads = NULL, plusCVG = NULL, minusCVG = NULL,
      size = 100L, up = 10000L, down = NULL, ...)

### Arguments

`features` | A GRanges object representing a set of genomic coordinates. The meta-plot will be centered on the transcription start site (TSS)
`reads` | A GRanges object representing a set of mapped reads. Instead of 'reads', 'plusCVG' and 'minusCVG' can be used Default: NULL
`plusCVG` | An IntegerRangesList object for reads with '+' strand.
`minusCVG` | An IntegerRangesList object for reads with '-' strand.
`size` | The size of the moving window.
`up` | Distance upstream of each features to align and histogram. Default: 10 kb.
`down` | Distance downstream of each features to align and histogram. If NULL, same as up. Default: NULL.
`...` | Extra argument passed to mclapply

### Value

Returns a integer-Rle representing the 'typical' signal centered on a point of interest.

### Author(s)

Charles G. Danko and Minho Chae

### Examples

    features <- GRanges("chr7", IRanges(1000, 1000), strand="+")
    reads <- GRanges("chr7", IRanges(start=c(1000:1004, 1100),
     width=rep(1, 6)), strand="+")
    mg <- metaGene(features, reads, size=4, up=10)

[Package groHMM version 1.14.0 Index]