easyRNASeq-island-methods: Identify expressed regions de-novo

In easyRNASeq: Count summarization and normalization for RNA-Seq data

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 These functions are now outdated and would need to be actualized.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

## S4 method for signature '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

Details

... are for providing additional options to the hist plot function.

Value

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

Author(s)

Nicolas Delhomme

Examples

	## Not run: 
	# NOTE that this function might need to be actualized
	obj <- new('RNAseq',
		organismName="Dmelanogaster",
		readLength=36L,
		chrSize=as.list(seqlengths(Dmelanogaster))
		)

 # fetch the example data
 bamFilePath <- fetchData("ACACTG.bam")

	obj <- fetchCoverage(obj,format="bam",filename=bamFilePath)

	obj <- findIslands(
			obj,
			max.gap=10L,
			min.cov=10L,
			min.length=200L)
	
## End(Not run)

easyRNASeq documentation built on April 30, 2020, 2 a.m.