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, keep.names = TRUE)

### Arguments

`grl` | a `GRangesList` object
`faFile` | `FaFile`, BSgenome, fasta/index file path or an ORFik `experiment`. This file is usually used to find the transcript sequences from some GRangesList.
`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.

### Details

A wrapper around `extractTranscriptSeqs` that works for DNAStringSet and ORFik `experiment` input. 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()`, `extendLeaders()`, `extendTrailers()`, `reduceKeepAttr()`, `tile1()`, `windowPerGroup()`

[Package ORFik version 1.14.7 Index]