metaGeneMatrix {groHMM} | R Documentation

## Returns a matrix, with rows representing read counts across a specified gene, or other features of interest.

### Description

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

### Usage

    metaGeneMatrix(features, reads, size = 50, up = 1000, down = up,
      debug = FALSE, ...)

### Arguments

`features` | A GRanges object representing a set of genomic coordinates.
`reads` | A GRanges object representing a set of mapped reads.
`size` | The size of the moving window.
`up` | Distance upstream of each f to align and histogram Default: 1 kb.
`down` | Distance downstream of each f to align and histogram Default: same as up.
`debug` | If set to TRUE, provides additional print options. Default: FALSE
`...` | Extra argument passed to mclapply

### Value

Returns a vector representing the 'typical' signal across genes of different length.

### Author(s)

Charles G. Danko and Minho Chae

[Package groHMM version 1.24.0 Index]