validate,BamFile-method {easyRNASeq}

R Documentation

Extension of the Rsamtools package

Description

Describes extensions to the Rsamtools package.

• For BamFile and BamFileList objects:

  • validate validates a BamFile or BamFileList object.

Usage

## S4 method for signature 'BamFile'
validate(obj, header = TRUE, cross.validation = TRUE)

Arguments

obj	An object of the BamFile or BamFileList class
header	a boolean to (de)activate the check for a BAM header
cross.validation	a boolean - only valid for BamFileList objects - to (de)activate the cross validation of all the BAM files header

Details

validate checks whether the BAM file exists and if a BAI index is present.

Value

validate returns invisibly a vector of boolean. Fails anyway if any file is missing.

Author(s)

Nicolas Delhomme

See Also

• BamFile

• BamFileList

Examples

# retrieve the data
tdir <- tutorialData()

# get the bam file path from the Bioc cache
filenames <- dir(tdir,pattern="[A,C,T,G]{6}\\.bam$",full.names=TRUE)

# retrieve the index from the Bioc cache too
inxnames <- sapply(paste0(sub(".*_","",basename(filenames)),".bai"),fetchData)

bfl <-BamFileList(filenames,index=inxnames)

validate(bfl)

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