read.prediction: Import the output of LTRharvest or LTRdigest

In HajkD/LTRpred: De novo functional annotation of retrotransposons

Import the output of LTRharvest or LTRdigest

Description

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

Usage

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(s)

Hajk-Georg Drost

Examples

## Not run: 
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)


## End(Not run)

HajkD/LTRpred documentation built on April 22, 2022, 4:35 p.m.