runAdmixture: runAdmixture

In esteinig/netview: Mutual k-Nearest-Neighbour Networks for Population Analysis

Description

Convenience function for running Admixture.

Usage

runAdmixture(filePath="/home/esteinig/admixture/butterflyfish.bed", K=1:10, processors=1, crossValidation=20, plotValidation=FALSE)

Arguments

filePath	Path to input files, either '.bed', '.ped' or '.geno' (see Admixture Manual)
K	Range of K for Admixture [ int vector, 1:10]
processors	Number of processors for analysis [ int, 1 ]
crossValidation	Number of cross-validation error iterations [ int, 20 ]
plotValidation	Return plot of cross-validation error across runs [ bool, FALSE ]
admixturePath	Path to admixture executable [ str, NULL ]

Details

Admixture executable can be in $PATH. If this is not working, you can specify the full path to the executable in admixturePath. For examples and tutorials, please see our GitHub Repository: https://github.com/esteinig/netview

Value

K-named vector containing cross-validation errors or plot of cross-validation error across K.

esteinig/netview documentation built on Feb. 8, 2022, 7:17 a.m.