Zeros in p values in snmf analysis from LEA packge
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Entering edit mode
Hanan • 0
@c51d74dc
Last seen 1 day ago
Israel

I took a data.frame (DF2) that contains a numeric genotypic data in the 012 format. and transformed it to a geno class object to run snmf analysis:

write.geno(DF2,"srr_wild.geno")

And run the analysis

project = snmf("srr_wild.geno", K = 1:10, entropy = TRUE, repetitions = 10, project = "new",ploidy = 2)

According to the analysis, I selected k=4. Then I ran the following:

p = snmf.pvalues(project,
             entropy = TRUE,
             ploidy = 2,
             K = 4)

I got p-values of 0

sum(p$pvalues==0)

557

Is it expected in this analysis to get zeros for p-values? Thank you

LEA snmf • 34 views
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