expressedGenes {groHMM} | R Documentation

## Function identifies expressed features using the methods introduced in Core, Waterfall, Lis; Science, Dec. 2008.

### Description

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

### Usage

    expressedGenes(features, reads, Lambda = NULL, UnMap = NULL,
      debug = FALSE, ...)

### Arguments

`features` | A GRanges object representing a set of genomic coordinates. The meta-plot will be centered on the start position. There can be optional "ID" column for gene ids.
`reads` | A GRanges object representing a set of mapped reads.
`Lambda` | Measurement of assay noise. Default: 0.04 reads/ kb in a library of 10,751,533 mapped reads. (background computed in Core, Waterfall, Lis. (2008) Science.).
`UnMap` | List object representing the position of un-mappable reads. Default: not used.
`debug` | If set to true, returns the number of positions. Default: FALSE.
`...` | Extra argument passed to mclapply

### Value

Returns a data.frame representing the expression p.values for features of interest.

### Author(s)

Charles G. Danko

[Package groHMM version 1.21.0 Index]