pausingIndex: Returns the pausing index for different genes. TODO:...

In coregenomics/groHMM: GRO-seq Analysis Pipeline

Description

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

Usage

pausingIndex(features, reads, size = 50, up = 1000, down = 1000,
  BPPARAM = bpparam())

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).
BPPARAM	Registered backend for BiocParallel. Default: BiocParallel::bpparam()

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

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

coregenomics/groHMM documentation built on May 7, 2019, 7:57 a.m.