Remove all non-phylogentically informative loci
This function will facilitate in removing phylogenetically uninformative loci
The user has the ability to define what uninformative means by setting a
cutoff value for either percentage of differentiating genotypes or minor
informloci(pop, cutoff = 2/nInd(pop), MAF = 0.01, quiet = FALSE)
This function will remove uninformative loci using a traditional MAF
isPoly from adegenet) as well
as analyzing the number of observed genotypes in a locus. This is important
for clonal organisms that can have fixed heterozygous sites not detected by
genind object with user-defined informative loci.
This will have a few side effects that affect certain analyses. First, the number of multilocus genotypes might be reduced due to the reduced number of markers (if you are only using a genind object). Second, if you plan on using this data for analysis of the index of association, be sure to use the standardized version (rbarD) that corrects for the number of observed loci.
Zhian N. Kamvar
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# We will use a dummy data set to demonstrate how this detects uninformative # loci using both MAF and a cutoff. genos <- c("A/A", "A/B", "A/C", "B/B", "B/C", "C/C") v <- sample(genos, 100, replace = TRUE) w <- c(rep(genos, 99), genos) # found by cutoff x <- c(rep(genos, 98), genos, genos) # found by MAF y <- c(rep(genos, 99), genos) # found by both z <- sample(genos, 100, replace = TRUE) dat <- df2genind(data.frame(v = v, w = w, x = x, y = y, z = z), sep = "/") informloci(dat) ## Not run: # Ignore MAF informloci(dat, MAF = 0) # Ignore cutoff informloci(dat, cutoff = 0) # Real data data(H3N2) informloci(H3N2) ## End(Not run)
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