pred2gff: Format LTR prediction data to GFF3 file format

In HajkD/LTRpred: De novo functional annotation of retrotransposons

Format LTR prediction data to GFF3 file format

Description

This function formats the LTR prediction data.frame generated by LTRharvest, LTRdigest, or LTRpred to a data.frame in GFF3 file format.

Usage

pred2gff(LTR.data, output = "output.gff", program = "LTRpred")

Arguments

LTR.data	the LTR prediction data.frame generated by LTRharvest, LTRdigest, or LTRpred.
output	filename of the output GFF file.
program	program used to generate the prediction table, e.g. program = "LTRpred", program = "LTRdigest", or program = "LTRharvest".

Details

The GFF3 file format is defined by: chromosome; start; end; name; columns.

Author(s)

Hajk-Georg Drost

References

http://www.ensembl.org/info/website/upload/gff.html

Examples

gff.file <- system.file("TAIR10_chr_all_LTRdigestPrediction.gff",
                        package = "LTRpred")
tabout.file <- system.file("TAIR10_chr_all-ltrdigest_tabout.csv"
                           ,package = "LTRpred")
LTRfile <- read.prediction(gff.file,tabout.file, program = "LTRdigest")

# generate GFF file
pred2gff(LTRfile$ltr.retrotransposon, output = "test.gff")

HajkD/LTRpred documentation built on April 22, 2022, 4:35 p.m.