read.zscore {LEA} | R Documentation |
lfmm
Read the output file from lfmm
. This is an internal function.
Zscores of a run can be accessed using the function z.scores
.
read.zscore(input.file)
input.file |
a character string containing a path to the output of |
R |
A matrix containing the |
Eric Frichot
### 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")