setClass("region.stats", representation(
######## Pops for each Test Module
Pop_Neutrality = "list",
Pop_FSTN = "list",
Pop_FSTH = "list",
Pop_Linkage = "list",
Pop_MK = "list",
genename = "list",
nucleotide.diversity = "list",
haplotype.diversity = "list",
haplotype.counts = "list" , # sfreqh
minor.allele.freqs = "list", # JFD
biallelic.structure = "list", # SXX
linkage.disequilibrium = "list", # Link
site.FST = "list",
missing.freqs = "list",
nuc.diversity.between = "list",
nuc.diversity.within = "list",
D = "list", #Patterson's D
df = "list", #df
TVmatrix = "list"
))
#"THETA","S (THETA)","T (THETA)","SA (THETA)","TA (THETA)","FL (THETA)","L (THETA)","FW (THETA)"
#"FREQUENCY (THETA) VALUES","Watterson Frequency","Tajima Frequency","Achaz, Watterson Frequency","Achaz, Tajima Frequency","Fu & Li
# Frequency","Zeng Frequency","Fay & Wu Frequency",
#### SHOW ######
setMethod("show", "region.stats",
function(object){
cat("-----\n")
cat("SLOTS:\n")
cat("-----\n")
out <- data.frame(Slots=c("nucleotide.diversity","haplotype.diversity","haplotype.counts", "minor.allele.freqs","linkage.disequilibrium","biallelic.structure","site.FST","missing.freqs","nuc.diversity.between","nuc.diversity.within","D","df"),
Description=c(
" Nucleotide diversity","Haplotype diversity","Haplotype distribution","Minor allele frequencies","Linkage disequilibrium","Shared and fixed polymorphisms","SNP-wise FST","Missing nucleotides","dxy","pi_within","Patterson's D","Distance Fraction"),
Module=c("FST","FST","FST","Detail","Linkage","Detail","Detail","count.unknowns","diversity.stats.between","diversity.stats","introgression.stats","introgression.stats"))
print(out)
cat("\n---------------\n")
cat("These are the Slots (class region.data) \n")
})
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