metaGene: Returns a histogram of the number of reads in each section of...

Description Usage Arguments Value Author(s) Examples

Description

Supports parallel processing using mclapply in the 'parallel' package. To change the number of processors, set the option 'mc.cores'.

Usage

1
2
metaGene(features, reads = NULL, plusCVG = NULL, minusCVG = NULL,
  size = 100L, up = 10000L, down = NULL, ...)

Arguments

features

A GRanges object representing a set of genomic coordinates. The meta-plot will be centered on the transcription start site (TSS)

reads

A GRanges object representing a set of mapped reads. Instead of 'reads', 'plusCVG' and 'minusCVG' can be used Default: NULL

plusCVG

A RangesList object for reads with '+' strand.

minusCVG

A RangesList object for reads with '-' strand.

size

The size of the moving window.

up

Distance upstream of each features to align and histogram. Default: 10 kb.

down

Distance downstream of each features to align and histogram. If NULL, same as up. Default: NULL.

...

Extra argument passed to mclapply

Value

Returns a integer-Rle representing the 'typical' signal centered on a point of interest.

Author(s)

Charles G. Danko and Minho Chae

Examples

1
2
3
4
features <- GRanges("chr7", IRanges(1000, 1000), strand="+")
reads <- GRanges("chr7", IRanges(start=c(1000:1004, 1100),
 width=rep(1, 6)), strand="+")
mg <- metaGene(features, reads, size=4, up=10)


Search within the groHMM package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.