This function reads the output of the ORFpred
function and stores the
sequence id and number of predicted ORFs in a data.frame
object.
read.orfs(input.file)
input.file | fasta file generated by |
---|
A data.frame
object storing the seq.id
, orfs
(number of predicted ORFs), start
, and end
of the predicted LTRs.
The file generated by ORFpred
is parsed by this function
and returned as data.frame
object.
Hajk-Georg Drost
# read an example prediction file generated by PredictORFs() ORFPred <- read.orfs(system.file("nt.fa",package = "LTRpred")) head(ORFPred) #> # A tibble: 6 × 2 #> seq.id orfs #> <chr> <dbl> #> 1 1_CHROMOSOME_dumped__10696719_10701589 2 #> 2 1_CHROMOSOME_dumped__11148084_11152830 1 #> 3 1_CHROMOSOME_dumped__11284903_11295619 2 #> 4 1_CHROMOSOME_dumped__11339006_11344662 1 #> 5 1_CHROMOSOME_dumped__11346530_11355061 2 #> 6 1_CHROMOSOME_dumped__11697950_11705480 1