easyRNASeq (version 2.8.2)

easyRNASeq island methods: Identify expressed regions de-novo

Description

Process the coverage to locate regions with a minimum coverage (min.cov). If regions are separated by a gap shorter than a maximum length (max.gap), they are unified. Only islands longer than min.length are returned. These functions are now outdated and would need to be actualized.

Usage

## S3 method for class 'RNAseq':
findIslands(obj, max.gap = integer(1), min.cov = 1L,
  min.length = integer(1), plot = TRUE, ...)

Arguments

obj

An object of class RNAseq

max.gap

Maximum gap between two peaks to build an island

min.cov

Minimum coverage for an island to be returned

min.length

Minimum size of an island to be returned

plot

If TRUE, draw plots of coverage distribution. Help the user to select an appropriate value for the minimum coverage.

...

See details

Value

• An RNAseq object with the readIsland slot set with a RangedData containing the selected islands and the readCount slot actualized with a list containing the count table per island.

code

hist

Details

...

Examples

## NOTE that this function might need to be actualized
	obj <- new('RNAseq',
		organismName="Dmelanogaster",
		readLength=36L,
		chrSize=as.list(seqlengths(Dmelanogaster))
		)

	obj <- fetchCoverage(
			obj,
			format="bam",
                        filename=system.file(
				"extdata",
				"ACACTG.bam",
                            	package="RnaSeqTutorial")
			)

	obj <- findIslands(
			obj,
			max.gap=10L,
			min.cov=10L,
			min.length=200L)