LEA (version 1.4.0)

read.zscore: Read the output files of lfmm

Description

Read the output file from lfmm. This is an internal function. Zscores of a run can be accessed using the function z.scores.

Usage

read.zscore(input.file)

Arguments

input.file

a character string containing a path to the output of lfmm.

Value

R

A matrix containing the lfmm results with one line per SNP. The first column is the zscore. The second column is the -log10(p-value). The third column is the p-value.

See Also

zscore.format lfmm

Examples

### Example of analyses using lfmm ###

data("tutorial")
# creation of the genotype file, genotypes.lfmm.
# It contains 400 SNPs for 50 individuals.
write.lfmm(tutorial.R, "genotypes.lfmm")
# creation of the environment file, gradient.env.
# It contains 1 environmental variable for 40 individuals.
write.env(tutorial.C, "gradients.env")

################
# runs of lfmm #
################

# main options, K: (the number of latent factors), 
#           CPU: the number of CPUs.

# Toy runs with K = 3 and 2 repetitions.
# around 15 seconds per run.
project = NULL
project = lfmm("genotypes.lfmm", "gradients.env", K = 3,
        iterations = 6000, burnin = 3000, project = "new")

res = read.zscore("./genotypes_gradients.lfmm/K3/run1/genotypes_r1_s1.3.zscore")