z.scores {LEA} | R Documentation |
Return the lfmm
output matrix of zscores for the chosen runs with K
latent factors, the d-th variable and the all option. For an example, see
lfmm
.
z.scores (object, K, d, all, run)
object |
A lfmmProject object. |
K |
The number of latent factors. |
d |
The d-th variable. |
all |
A Boolean option. If true, the run with all variables at the same time. If false, the runs with each variable separately. |
run |
A list of chosen runs. |
res |
A matrix containing a vector of z-scores for the chosen runs per column. |
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, repetitions = 2, iterations = 6000, burnin = 3000, project = "new") # get the z-scores for all runs for K = 3 z = z.scores(project, K = 3) # get the z-scores for the 2nd run for K =3 z = z.scores(project, K = 3, run = 2) # remove remove.lfmmProject("genotypes_gradients.lfmmProject")