Import the output of LTRharvest or LTRdigest — read.prediction • LTRpred

This function imports the output files generated by LTRharvest or LTRdigest.

read.prediction(
  gff.file = NULL,
  tabout.file,
  program = "LTRdigest",
  ltr.fasta = NULL,
  inner.seq.fasta = NULL,
  data = NULL,
  similarity.bin = 2,
  min.sim = NULL
)

Arguments

gff.file	path to GFF file generated by either `LTRharvest`, `LTRdigest`, or `LTRpred`.
tabout.file	path to `*_tabout.csv` file generated by either `LTRdigest` or or `LTRpred`.
program	prediction program used to generate the corresponding GFF file. Either `program = "LTRharvest"`, `program = "LTRdigest"`, or `program = "LTRpred"`.
ltr.fasta	fasta file generated by either `LTRdigest` or or `LTRpred` storing the sequences of the predicted LTR retrotransposons (e.g. `*-ltrdigest_complete.fas`).
inner.seq.fasta	path to the `*_BetweenLTRSeqs.fsa` fasta file returned by `LTRharvest` in caste `program = "LTRharvest"` is specified.
data	the `data.frame` returned by either `LTRharvest`, `LTRdigest`, or `LTRpred` that can be used to modify for example `similarity.bin` and `min.sim` within this table.
similarity.bin	resolution of similarity binning. E.g. binning 98%-100% into 0.5% intervals would be `similarity.bin = 0.5`.
min.sim	minimum similarity between LTRs that can shall be considered for visualization.

Author

Hajk-Georg Drost

Examples

if (FALSE) {
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")

# look at results
str(LTRfile$ltr.retrotransposon)

}