Format LTR prediction data to CSV file format

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

pred2csv(LTR.data, output = "output.csv")

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

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")
#> 
#> Input:  /private/var/folders/yn/mgwl8_b56hz4v2c2vlfxj07w00076j/T/Rtmp9EQNCE/temp_libpath123013836f1/LTRpred/TAIR10_chr_all_LTRdigestPrediction.gff  -> Row Number:  3323
#> Remove 'NA' -> New Row Number:  3323
#> (1/8) Filtering for repeat regions has been finished.
#> (2/8) Filtering for LTR retrotransposons has been finished.
#> (3/8) Filtering for inverted repeats has been finished.
#> (4/8) Filtering for LTRs has been finished.
#> (5/8) Filtering for target site duplication has been finished.
#> (6/8) Filtering for primer binding site has been finished.
#> (7/8) Filtering for protein match has been finished.
#> (8/8) Filtering for RR tract has been finished.

# generate csv file
pred2csv(LTRfile$ltr.retrotransposon)