get.tRNAprecursor {tRNAscanImport} | R Documentation |
get.tRNAprecursor
retrieves tRNA precursor sequences from genomic
sequences. The length of 5'- and 3'-overhangs can be specifid individually.
The output is checked for validity against the tRNA sequences as reported by
tRNAscan.
The chromosomes names of tRNAscan input and genome sequences must be compatible.
get.tRNAprecursor( input, genome, add.5prime = 50L, add.3prime = add.5prime, trim.intron = FALSE )
input |
a compatible |
genome |
a |
add.5prime, add.3prime |
the length of overhangs as a single integer
value each. (default |
trim.intron |
|
a DNAStringSet
object, containing the precursor sequences.
library(BSgenome.Scerevisiae.UCSC.sacCer3) file <- system.file("extdata", file = "yeast.tRNAscan", package = "tRNAscanImport") gr <- tRNAscanImport::import.tRNAscanAsGRanges(file) genome <- getSeq(BSgenome.Scerevisiae.UCSC.sacCer3) names(genome) <- c(names(genome)[-17],"chrmt") get.tRNAprecursor(gr, genome) # this produces an error since the seqnames do not match ## Not run: genome <- BSgenome.Scerevisiae.UCSC.sacCer3 names(genome) <- c(names(genome)[-17],"chrmt") get.tRNAprecursor(gr, genome) ## End(Not run) # ... but it can also be fixed genome <- BSgenome.Scerevisiae.UCSC.sacCer3 seqnames(genome) <- c(seqnames(genome)[-17],"chrmt") get.tRNAprecursor(gr, genome)