Format LTR prediction data to GRages object

Source: R/pred2GRanges.R

This function formats the LTR prediction data.frame generated by LTRpred to a GRages object.

pred2GRanges(LTR.data, similarity.threshold = 95)

Arguments

LTR.data

the LTR prediction data.frame generated by LTRpred.
similarity.threshold

the LTR similarity threshold that shall be used to define young and old retrotransposons.

Details

The GRages object is defined by the following columns:

  • chromosome

  • start

  • end

  • strand

  • element_name

  • ltr_similarity

  • orfs

  • age

Author

Hajk-Georg Drost