Detect LTR retrotransposons that are potential jumpers

Source: R/filter.jumpers.R

This function applies specific filter criteria to screen for LTR retrotransposons predicted by LTRpred that are potentially able to transpose due to their sequence features.

filter.jumpers(LTRpred.tbl, ltr.similarity = 95, strategy = "conservative")

Arguments

LTRpred.tbl

a data.frame generated by LTRpred.
ltr.similarity

LTR similarity threshold. Default is ltr_similarity = 95.
strategy

filter strategy: either conservative, liberal, or between.

Details

This ...

Filter strategy

  • conservative :

  • liberal :

  • between :

See also

LTRpred

Author

Hajk-Georg Drost

Examples

if (FALSE) {
# generate de novo LTR transposon prediction
pred <- LTRpred(genome.file = "TAIR10_chr_all.fas",
                trnas       = "plantRNA_Arabidopsis.fsa",
                hmms        = "hmm_*")
                
# detect potential jumpers               
filter.jumpers(pred)
}