Estimate retrotransposon insertion age in Mya based on 5 prime and 3 prime LTR sequence homology

Source: R/ltr_age_estimation.R

This function implements diverse metrics to roughly estimate the insertion age in Mya based on 5 prime and 3 prime LTR sequence homology.

ltr_age_estimation(
  pred,
  ltr_seqs_3_prime,
  ltr_seqs_5_prime,
  model = "K80",
  mutation_rate = 1.3 * 1e-07
)

Arguments

pred

a prediction file generated with LTRpred.
ltr_seqs_3_prime

file path to a fasta file storing the sequences of the respective 3 prime LTR (e.g. as annotatted by LTRpred).
ltr_seqs_5_prime

file path to a fasta file storing the sequences of the respective 5 prime LTR (e.g. as annotatted by LTRpred).
model

a model as specified in dist.dna: a character string specifying the evolutionary model to be used - must be one of

  • K80 (the default)

  • raw

  • N

  • TS

  • TV

  • JC69

  • F81

  • K81

  • F84

  • BH87

  • T92

  • TN93

  • GG95

  • logdet

  • paralin
mutation_rate

a mutation rate per site per year. For retrotransposons the default is \(mutation_rate = 1.3 * 10E-8\) (Wicker and Keller, 2007).

Author

Hajk-Georg Drost

Examples

if (FALSE) {
ltr_pred <- LTRpred::read.ltrpred(
          system.file("Hsapiens_ChrY_LTRpred_DataSheet.tsv", 
          package = "LTRpred"))
# define file path to fasta file storing 3 prime LTR sequences
ltr_seqs_3_prime <- system.file("Hsapiens_ChrY-ltrdigest_3ltr.fas", package = "LTRpred")
ltr_seqs_5_prime <- system.file("Hsapiens_ChrY-ltrdigest_5ltr.fas", package = "LTRpred")
# estimate insertion age based on 3 prime and 5 prime LTR homology using the K80 model
Hsapiens_ltr_age <- LTRpred::ltr_age_estimation(ltr_pred, ltr_seqs_3_prime, ltr_seqs_5_prime)
# look at results
Hsapiens_ltr_age
}