filter.jumpers: Detect LTR retrotransposons that are potential jumpers

In HajkD/LTRpred: De novo functional annotation of retrotransposons

Detect LTR retrotransposons that are potential jumpers

Description

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.

Usage

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 :

Author(s)

Hajk-Georg Drost

See Also

LTRpred

Examples

## Not run: 
# 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)

## End(Not run)

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