This function will facilitate in removing phylogenetically uninformative loci
from a genclone or genind object.
The user has the ability to define what uninformative means by setting a
cutoff value for either percentage of differentiating genotypes or minor
allele frequency.
Usage
informloci(pop, cutoff = 2/nInd(pop), MAF = 0.01, quiet = FALSE)Arguments
- pop
- cutoff
numeric. A number from 0 to 1 defining the minimum number of differentiating samples.- MAF
numeric. A number from 0 to 1 defining the minimum minor allele frequency. This is passed as thethreshparameter ofisPoly.- quiet
logical. Whenquiet = TRUE(default), messages indicating the loci removed will be printed to screen. Whenquiet = FALSE, nothing will be printed to screen.
Details
This function will remove uninformative loci using a traditional MAF
cutoff (using 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
MAF methods.
Note
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.
Examples
# 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[2], 99), genos[3]) # found by cutoff
x <- c(rep(genos[1], 98), genos[3], genos[2]) # found by MAF
y <- c(rep(genos[1], 99), genos[2]) # 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)
#> cutoff value: 2 % ( 2 samples ).
#> MAF : 0.01
#>
#> Found 3 uninformative loci
#> ============================
#> 2 loci found with a cutoff of 2 samples :
#> w, y
#> 2 loci found with MAF < 0.01 :
#> x, y
#> /// GENIND OBJECT /////////
#>
#> // 100 individuals; 2 loci; 6 alleles; size: 14.6 Kb
#>
#> // Basic content
#> @tab: 100 x 6 matrix of allele counts
#> @loc.n.all: number of alleles per locus (range: 3-3)
#> @loc.fac: locus factor for the 6 columns of @tab
#> @all.names: list of allele names for each locus
#> @ploidy: ploidy of each individual (range: 2-2)
#> @type: codom
#> @call: .local(x = x, i = i, j = j, loc = ..1, drop = drop)
#>
#> // Optional content
#> - empty -
# \dontrun{
# Ignore MAF
informloci(dat, MAF = 0)
#> cutoff value: 2 % ( 2 samples ).
#> MAF : 0
#>
#> Found 2 uninformative loci
#> ============================
#> 2 loci found with a cutoff of 2 samples :
#> w, y
#> 0 loci found with MAF < 0
#> /// GENIND OBJECT /////////
#>
#> // 100 individuals; 3 loci; 9 alleles; size: 16.5 Kb
#>
#> // Basic content
#> @tab: 100 x 9 matrix of allele counts
#> @loc.n.all: number of alleles per locus (range: 3-3)
#> @loc.fac: locus factor for the 9 columns of @tab
#> @all.names: list of allele names for each locus
#> @ploidy: ploidy of each individual (range: 2-2)
#> @type: codom
#> @call: .local(x = x, i = i, j = j, loc = ..1, drop = drop)
#>
#> // Optional content
#> - empty -
# Ignore cutoff
informloci(dat, cutoff = 0)
#> cutoff value: 0 % ( 0 samples ).
#> MAF : 0.01
#>
#> Found 2 uninformative loci
#> ============================
#> 0 loci found with a cutoff of 0 samples
#> 2 loci found with MAF < 0.01 :
#> x, y
#> /// GENIND OBJECT /////////
#>
#> // 100 individuals; 3 loci; 9 alleles; size: 16.5 Kb
#>
#> // Basic content
#> @tab: 100 x 9 matrix of allele counts
#> @loc.n.all: number of alleles per locus (range: 3-3)
#> @loc.fac: locus factor for the 9 columns of @tab
#> @all.names: list of allele names for each locus
#> @ploidy: ploidy of each individual (range: 2-2)
#> @type: codom
#> @call: .local(x = x, i = i, j = j, loc = ..1, drop = drop)
#>
#> // Optional content
#> - empty -
# Real data
data(H3N2)
informloci(H3N2)
#> cutoff value: 0.105097214923805 % ( 2 samples ).
#> MAF : 0.01
#>
#> Found 5 uninformative loci
#> ============================
#> 1 locus found with a cutoff of 2 samples :
#> 597
#> 5 loci found with MAF < 0.01 :
#> 42, 313, 433, 597, 915
#> /// GENIND OBJECT /////////
#>
#> // 1,903 individuals; 120 loci; 322 alleles; size: 3.3 Mb
#>
#> // Basic content
#> @tab: 1903 x 322 matrix of allele counts
#> @loc.n.all: number of alleles per locus (range: 2-4)
#> @loc.fac: locus factor for the 322 columns of @tab
#> @all.names: list of allele names for each locus
#> @ploidy: ploidy of each individual (range: 1-1)
#> @type: codom
#> @call: .local(x = x, i = i, j = j, loc = ..1, drop = drop)
#>
#> // Optional content
#> @other: a list containing: x xy epid
#>
# }