expressedGenes: Function identifies expressed features using the methods...

In groHMM: GRO-seq Analysis Pipeline

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

groHMM documentation built on Nov. 8, 2020, 8:09 p.m.