import.tRNAscanAsGRanges: Importing a tRNAscan output file as a GRanges object

In FelixErnst/tRNAscanImport: Importing a tRNAscan-SE result file as GRanges object

Importing a tRNAscan output file as a GRanges object

Description

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.

tRNAscanID generates a unique tRNA ID, which is like the format used in the SGD annotation

t*AminoAcidSingleLetter*(*Anticodon*)*ChromosomeIdentifier**optionalNumberIfOnTheSameChromosome*

Example: tP(UGG)L or tE(UUC)E1.

Usage

import.tRNAscanAsGRanges(input, as.GFF3 = FALSE, trim.intron = TRUE)

tRNAscan2GFF(input)

tRNAscanID(input)

Arguments

input	import.tRNAscanAsGRanges: a tRNAscan-SE input file tRNAscan2GFF: a compatible GRanges object such as the output of import.tRNAscanAsGRanges
as.GFF3	optional logical for import.tRNAscanAsGRanges: returns a gff3 compatible GRanges object directly. (default: as.GFF3 = FALSE)
trim.intron	optional logical for import.tRNAscanAsGRanges: remove intron sequences. This changes the tRNA length reported. To retrieve the original length fo the tRNA gene, use the width() function on the GRanges object. (default: trim.intron = TRUE)

Value

a GRanges object

References

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.

Examples

gr <- import.tRNAscanAsGRanges(system.file("extdata", 
                               file = "yeast.tRNAscan", 
                               package = "tRNAscanImport"))
gff <- tRNAscan2GFF(gr)
identical(gff,import.tRNAscanAsGRanges(system.file("extdata", 
                               file = "yeast.tRNAscan", 
                               package = "tRNAscanImport"),
                               as.GFF3 = TRUE))

FelixErnst/tRNAscanImport documentation built on March 29, 2024, 5:44 p.m.