pausingIndex: Returns the pausing index for different genes. TODO:...
In groHMM: GRO-seq Analysis Pipeline

Description Usage Arguments Value Author(s) Examples

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

1 2	pausingIndex(features, reads, size = 50, up = 1000, down = 1000, UnMAQ = NULL, debug = FALSE, ...)

`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

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

Returns the pausing index for different genes.

Charles G. Danko and Minho Chae.

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