gl.collapse: Collapses a distance matrix by amalgamating populations with...

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Collapses a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold

Description

This script takes a file generated by gl.fixed.diff and amalgamates populations with distance less than or equal to a specified threshold. The distance matrix is generated by gl.fixed.diff().

The script then applies the new population assignments to the genlight object and recalculates the distance and associated matrices.

Usage

gl.collapse(fd, tpop = 0, tloc = 0, pb = FALSE, verbose = NULL)

Arguments

fd	Name of the list of matrices produced by gl.fixed.diff() [required].
tpop	Threshold number of fixed differences above which populations will not be amalgamated [default 0].
tloc	Threshold defining a fixed difference (e.g. 0.05 implies 95:5 vs 5:95 is fixed) [default 0].
pb	If TRUE, show a progress bar on time consuming loops [default FALSE].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

Value

A list containing the gl object x and the following square matrices:

1. $gl – the new genlight object with populations collapsed;

2. $fd – raw fixed differences;

3. $pcfd – percent fixed differences;

4. $nobs – mean no. of individuals used in each comparison;

5. $nloc – total number of loci used in each comparison;

6. $expfpos – NA's, populated by gl.fixed.diff [by simulation]

7. $expfpos – NA's, populated by gl.fixed.diff [by simulation]

8. $prob – NA's, populated by gl.fixed.diff [by simulation]

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

Examples

 
fd <- gl.fixed.diff(testset.gl,tloc=0.05)
fd
fd2 <- gl.collapse(fd,tpop=1)
fd2
fd3 <- gl.collapse(fd2,tpop=1)
fd3

 fd <- gl.fixed.diff(testset.gl,tloc=0.05)
 fd2 <- gl.collapse(fd)

green-striped-gecko/dartR documentation built on Jan. 31, 2024, 10:14 a.m.