dist_long: Return evolutionary distance in long format

In andersgs/harrietr: Wrangle Phylogenetic Distance Matrices and Other Utilities

Description

This will take an alignment, will calculate the evolutionary distance between all pairs of sequence, and will transform the distance matrix to long format. It will remove upper triangle, and diagonal elements, so you end with only (n)*(n-1)/2 rows, where n are the total number of rows in the distance matrix.

Usage

dist_long(aln, order = NULL, dist = "N", tree = NULL)

Arguments

aln	An object of class matrix, it must be square
order	A character vector of size n with the order of the columns and rows (default: NULL)
dist	A string naming the model to calculate distances (accepted values are those in ape::dist.dna)
tree	An object of class phylo

Details

If a tree is optionally given, a fourth column is returned with the cophenetic distance across all elements of tree. It assumes the tree was generated from the alignment.

Value

A data.frame with three or four columns: (1) iso1; (2) iso2: (3) dist. If a tree is given then a fourth column (evol_dist) containig the distances from the tree is also supplied.

Examples

## Not run: 
data(woodmouse)
dist_df <- dist_long(woodmouse)

## End(Not run)

andersgs/harrietr documentation built on May 12, 2019, 2:41 a.m.