str2lfmm: Prepare Input Files for Latent Factor Mixed Modeling (LFMM)

In bouzidnm/tinker: Miscellaneous Functions for Data Cleaning, Formatting, and Visualization

Description

str2lfmm recodes biallelic SNP loci in STRUCTURE format to a format suitable for LFMM. An arbitrary vector of reference alleles is automatically chosen, though the reference can be specified by the user if known. str2lfmm accepts both diploid and haploid SNP data. Each diploid individual must be coded on two lines. Ambiguity codes must be removed and nucleotides must be coded as integers (e.g. A, T, C, G as 1, 2, 3, 4). Trait data (either phenotype or environmental variables) can also be included. Samples may be excluded by specifying using 'exclude,'

Usage

str2lfmm(str.data, trait.data, exclude)

Arguments

str.data	SNP data in STRUCTURE format
trait.data	Phenotype or environment data
exclude	Vector of sample IDs to exclude

Examples

str2lfmm(str.data = str.data,
trait.data = trait.data,
exclude = NULL)

bouzidnm/tinker documentation built on May 25, 2019, 11:31 p.m.