pausingIndex {groHMM} | R Documentation

## Returns the pausing index for different genes. TODO: DESCRIBE THE PAUSING INDEX.

### Description

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

### Usage

    pausingIndex(features, reads, size = 50, up = 1000, down = 1000,
      UnMAQ = NULL, 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.
`down` | Distance downstream of each f to align and histogram (NULL).
`UnMAQ` | Data structure representing the coordinates of all un-mappable regions in the genome.
`debug` | If set to TRUE, provides additional print options. Default: FALSE
`...` | Extra argument passed to mclapply

### Value

Returns a data.frame of the pausing indices for the input genes.

Returns the pausing index for different genes.

### Author(s)

Charles G. Danko and Minho Chae.

### Examples

    features <- GRanges("chr7", IRanges(2394474,2420377), strand="+")
     reads <- as(readGAlignments(system.file("extdata", "S0mR1.bam",
                 package="groHMM")), "GRanges")
     ## Not run:
     # pi <- pausingIndex(features, reads)

[Package groHMM version 1.24.0 Index]