Returns a matrix, with rows representing read counts across a specified gene, or other features of interest.

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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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

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