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

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Description

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

Usage

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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

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

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