promotor_divergence_of_orthologous_genes: Compute promotor sequence divergence of orthologous genes
In HajkD/orthologr: Comparative Genomics with R

View source: R/promotor_divergence_of_orthologous_genes.R

promotor_divergence_of_orthologous_genes

R Documentation

Compute promotor sequence divergence of orthologous genes

Description

This function computes the promotor sequence divergences of orthologous genes from a set of pairwise species comparisons. It allows to add this promotor divergence information to an pre-computed dNdS table generated with dNdS or generate_ortholog_tables_all.

Usage

promotor_divergence_of_orthologous_genes(
  promotor_folder,
  ortholog_tables_folder,
  model = "K80",
  ortholog_promotor_seq_output = NULL
)

Arguments

`promotor_folder`	a path to a folder containing promotor sequences in `fasta` format that were generated with `extract_upstream_promotor_seqs`.
`ortholog_tables_folder`	a path to a folder containing dNdS tables generated with `generate_ortholog_tables_all`
`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`
`ortholog_promotor_seq_output`	a path or name to an output folder where orthologous promotor sequences shall be stored.