validate,BamFile-method {easyRNASeq} | R Documentation |
Describes extensions to the Rsamtools package.
For BamFile
and
BamFileList
objects:
validate
validates a BamFile
or
BamFileList
object.
## S4 method for signature 'BamFile' validate(obj, header = TRUE, cross.validation = TRUE)
obj |
An object of the |
header |
a boolean to (de)activate the check for a BAM header |
cross.validation |
a boolean - only valid for
|
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
# 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)