getArborescence: Function to transform a distance matrix of observations into...

In Fraternalilab/BrepPhylo: BrepPhylo: R package for phylogenetic analysis of B cell repertoire

Function to transform a distance matrix of observations into a list of "Arc"s, a tuple defined in the python script "edmond_arborescence.py"

Description

Function to transform a distance matrix of observations into a list of "Arc"s, a tuple defined in the python script "edmond_arborescence.py"

Usage

getArborescence(distances, dfSubclass, germline)

Arguments

distances	Either a "dist" or a matrix with the observations.
dfSubclass	A two-column data frame holding: SeqID The sequence ID as used in the distance object. Class The isotype subclass of the observations.
germline	character, the sequence to be taken as the germline Note, that the germline has subclass type "germline" and observations without a valid subclass must be labelled 'NA' (will be ignored).

Value

A data frame with the columns "startID" (number of start), "endID" (number of end point), "weight" (weight of the arc), "startLabel" (the labels for the start IDs) and "endID" (the labels for the end IDs) for an arborescence minimum spanning tree.

Fraternalilab/BrepPhylo documentation built on Jan. 3, 2025, 10:03 a.m.