import.tRNAscanAsGRanges {tRNAscanImport} | R Documentation |
The function import.tRNAscanAsGRanges
will import a tRNAscan-SE output
file and return the information as a GRanges object. The reported
intron sequences are spliced from the result by default, but can also
returned as imported.
The function tRNAScan2GFF
formats the output of
import.tRNAscanAsGRanges
to be GFF3 compliant.
import.tRNAscanAsGRanges(input, as.GFF3 = FALSE, trim.intron = TRUE) tRNAscan2GFF(input)
input |
|
as.GFF3 |
optional logical for |
trim.intron |
optional logical for |
a GRanges object
Chan, Patricia P., and Todd M. Lowe. 2016. “GtRNAdb 2.0: An Expanded Database of Transfer Rna Genes Identified in Complete and Draft Genomes.” Nucleic Acids Research 44 (D1): D184–9. doi:10.1093/nar/gkv1309.
Lowe, T. M., and S. R. Eddy. 1997. “TRNAscan-Se: A Program for Improved Detection of Transfer Rna Genes in Genomic Sequence.” Nucleic Acids Research 25 (5): 955–64.
gr <- import.tRNAscanAsGRanges(system.file("extdata", file = "sacCer3-tRNAs.ss.sort", package = "tRNAscanImport")) gff <- tRNAscan2GFF(gr) identical(gff,import.tRNAscanAsGRanges(system.file("extdata", file = "sacCer3-tRNAs.ss.sort", package = "tRNAscanImport"), as.GFF3 = TRUE))