easyRNASeq (version 2.8.2)

easyRNASeq coverage methods: Compute the coverage from a Short Read Alignment file

Description

Computes the genomic reads' coverage from a read file in bam format or any format supported by ShortRead.

Usage

## S3 method for class 'RNAseq':
fetchCoverage(obj, format = c("aln", "bam"),
  filename = character(1), filter = srFilter(), type = "SolexaExport",
  chr.sel = c(), validity.check = TRUE, chr.map = data.frame(),
  ignoreWarnings = FALSE, gapped = TRUE, paired = FALSE,
  stranded = FALSE, bp.coverage = FALSE, ...)

Arguments

obj

An RNAseq object

format

The format of the reads, one of "aln","bam". If not "bam", all the types supported by the ShortRead package are supported too.

filename

The full path of the file to use

filter

The filter to be applied when loading the data using the "aln" format

type

The type of data when using the "aln" format. See the ShortRead package.

chr.sel

A vector of chromosome names to subset the final results.

validity.check

Shall UCSC chromosome name convention be enforced

chr.map

A data.frame describing the mapping of original chromosome names towards wished chromosome names. See details.

ignoreWarnings

set to TRUE (bad idea! they have a good reason to be there) if you do not want warning messages.

gapped

Is the bam file provided containing gapped alignments?

paired

Is the bam file containing PE reads?

stranded

Is the bam file from a strand specific protocol?

bp.coverage

a boolean that default to FALSE to decide whether coverage is to be calculated and stored by bp

...

additional arguments. See details

Value

• An RNAseq object. The slot readCoverage contains a SimpleRleList object representing a list of coverage vectors, one per chromosome.

pkg

• ShortRead
• Rsamtools

Details

...

See Also

Rle ShortRead:readAligned

Examples

library("RnaSeqTutorial")
	library(BSgenome.Dmelanogaster.UCSC.dm3)

	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")
			)