metaGeneMatrix: Returns a matrix, with rows representing read counts across a...

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

metaGeneMatrix(features, reads, size = 50, up = 1000, down = up,
  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 Default: 1 kb.
down	Distance downstream of each f to align and histogram Default: same as up.
debug	If set to TRUE, provides additional print options. Default: FALSE
...	Extra argument passed to mclapply

Value

Returns a vector representing the 'typical' signal across genes of different length.

Author(s)

Charles G. Danko and Minho Chae

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