dn_ds: dN/dS Average Ratio This function perform the dN/dS ratios...

In irycisBioinfo/PATO: Pangenome Analysis Toolkit

dN/dS Average Ratio This function perform the dN/dS ratios for each gene family of the pangenome. It uses the dnds() function of ape package. dnds() returns a dist object. That object if transformed to matrix. Diagonal values, and negative values are remove. Infinity values are transformed to a max value not infinite. Finally it obtains the mean of the matrix.

Description

This function needs mafft and/or blastn intalled in you system and available in the PATH.

Usage

dn_ds(mmseq, accnet, min_size = 5, n_cores, mode = "fast")

Arguments

mmseq	A mmseq object
accnet	The resulting accnet object of the mmseq object
min_size	Gene families smaller than this value are ingnored
n_cores	Number of cores to paralyse.
mode	Alignment mode c("fast",accurate")

irycisBioinfo/PATO documentation built on Oct. 19, 2023, 3:07 p.m.