phsc.get.basic.pairwise.relationships: Calculate basic pairwise relationships

View source: R/phyloscan.fun.private.R

phsc.get.basic.pairwise.relationshipsR Documentation

Calculate basic pairwise relationships

Description

This function calculates basic pairwise relationships of two individuals in any window. Several different relationship groups can be calculated, for example just using pairwise distance, or using both pairwise distance and topology to define likely pairs.

Usage

phsc.get.basic.pairwise.relationships(
  df,
  trmw.close.brl,
  trmw.distant.brl,
  verbose = TRUE
)

Arguments

df

data.table to which basic pairwise relationships will be added. Must contain columns with name 'ADJACENT','TYPE_RAW','PATRISTIC_DISTANCE','PATHS_12','PATHS_21'.

trmw.close.brl

Maximum patristic distance between any two read trees from both individuals in a window to classify the individuals as phylogenetically close.

trmw.distant.brl

Minimum patristic distance between any two read trees from both individuals in a window to classify the individuals as phylogenetically distant.

Value

input data.table with new relationship column TYPE_BASIC.


olli0601/Phyloscanner.R.utilities documentation built on March 24, 2024, 3:23 p.m.