easyRNASeq island methods {easyRNASeq} | R Documentation

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 These functions are now outdated and would need to be actualized.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

    ## 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)

[Package easyRNASeq version 2.30.0 Index]