Rsamtools-methods: Extension of the Rsamtools package
In easyRNASeq: Count summarization and normalization for RNA-Seq data

Description Usage Arguments Details Value Author(s) See Also Examples

Describes extensions to the Rsamtools package.

For BamFile and BamFileList objects:
- validate validates a BamFile or BamFileList object.

1 2	## S4 method for signature 'BamFile' validate(obj, header = TRUE, cross.validation = TRUE)

`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

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

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

Nicolas Delhomme

BamFile
BamFileList

# 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)