pred2tsv: Format LTR prediction data to TSV file format

In HajkD/LTRpred: De novo functional annotation of retrotransposons

Format LTR prediction data to TSV file format

Description

This function formats the LTR prediction data.frame generated by LTRharvest, LTRdigest, or LTRpred to a data.frame in CSV file format.

Usage

pred2tsv(LTR.data, output = "output.tsv")

Arguments

LTR.data	the LTR prediction data.frame generated by LTRharvest, LTRdigest, or LTRpred.
output	filename of the output CSV file.

Value

the LTR.data table in csv format saved to the hard drive.

Author(s)

Hajk-Georg Drost

Examples

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 csv file
pred2csv(LTRfile$ltr.retrotransposon)

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