Format LTR prediction data to GFF3 file format

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

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.

References

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

Author

Hajk-Georg Drost

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")
#> 
#> Input:  /private/var/folders/yn/mgwl8_b56hz4v2c2vlfxj07w00076j/T/Rtmp9EQNCE/temp_libpath123013836f1/LTRpred/TAIR10_chr_all_LTRdigestPrediction.gff  -> Row Number:  3323
#> Remove 'NA' -> New Row Number:  3323
#> (1/8) Filtering for repeat regions has been finished.
#> (2/8) Filtering for LTR retrotransposons has been finished.
#> (3/8) Filtering for inverted repeats has been finished.
#> (4/8) Filtering for LTRs has been finished.
#> (5/8) Filtering for target site duplication has been finished.
#> (6/8) Filtering for primer binding site has been finished.
#> (7/8) Filtering for protein match has been finished.
#> (8/8) Filtering for RR tract has been finished.

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