| txSeqsFromFa {ORFik} | R Documentation |
For each GRanges object, find the sequence of it from faFile or BSgenome.
txSeqsFromFa(grl, faFile, is.sorted = FALSE, keep.names = TRUE)
grl |
a |
faFile |
|
is.sorted |
a speedup, if you know the grl ranges are sorted |
keep.names |
a logical, default (TRUE), if FALSE: return as character vector without names. |
A small safety wrapper around extractTranscriptSeqs
For debug of errors do:
which(!(unique(seqnamesPerGroup(grl, FALSE))
This happens usually when the grl contains chromsomes that the fasta
file does not have. A normal error is that mitocondrial chromosome is
called MT vs chrM even though they have same seqlevelsStyle. The
above line will give you which chromosome it is missing.
a DNAStringSet of the transcript sequences
Other ExtendGenomicRanges:
asTX(),
coveragePerTiling(),
reduceKeepAttr(),
tile1(),
windowPerGroup()