txSeqsFromFa {ORFik}R Documentation

Get transcript sequence from a GrangesList and a faFile or BSgenome

Description

For each GRanges object, find the sequence of it from faFile or BSgenome.

Usage

txSeqsFromFa(grl, faFile, is.sorted = FALSE)

Arguments

grl

a GRangesList object

faFile

FaFile, BSgenome, fasta/index file path or an ORFik experiment. This file used to find the transcript sequences

is.sorted

a speedup, if you know the ranges are sorted

Details

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.

Value

a DNAStringSet of the transcript sequences

See Also

Other ExtendGenomicRanges: asTX(), coveragePerTiling(), overlapsToCoverage(), reduceKeepAttr(), tile1(), windowPerGroup()


[Package ORFik version 1.6.9 Index]