expressedGenes

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.

features

A GRanges object representing a set of mapped reads.

reads

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.).

Lambda

List object representing the position of un-mappable reads.
Default: not used.

UnMap

If set to true, returns the number of positions.
Default: FALSE.

debug


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


A pipeline for the analysis of GRO-seq data.

Minho Chae W Lee Kraus leekrausutsouthwesternedu

groHMM

GRO-seq Analysis Pipeline

expressedGenes function

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

expressedGenes: Function identifies expressed features using the methods introduced in Core, Waterfall, Lis; Science, Dec. 2008.

Description

Usage

Arguments

Value