pred2gff | R Documentation |
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")
LTR.data |
the LTR prediction |
output |
filename of the output GFF file. |
program |
program used to generate the prediction table, e.g. |
The GFF3 file format is defined by: chromosome; start; end; name; columns.
Hajk-Georg Drost
http://www.ensembl.org/info/website/upload/gff.html
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")
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