pred2bed | R Documentation |
This function formats the LTR prediction data.frame
generated by LTRharvest
, LTRdigest
, or LTRpred
to a data.frame
in BED
file format.
pred2bed(LTR.data, output = "output")
LTR.data |
the LTR prediction |
output |
filename of the output BED file. |
The BED file format is defined by: chromosome; start; end; name; columns.
Hajk-Georg Drost
http://www.ensembl.org/info/website/upload/bed.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 BED file pred2bed(LTRfile$ltr.retrotransposon)
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