[adegenet-forum] propShared Alleles
Jombart, Thibaut
t.jombart at imperial.ac.uk
Fri Jul 13 18:58:26 CEST 2012
Hello,
there was a bug in some old version of propShared. Are you using the latest version of adegenet (stable 1.3-4 or devel 1.3-5)?
Cheers
Thibaut
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Johannes Signer [j.m.signer at gmail.com]
Sent: 13 July 2012 17:39
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] propShared Alleles
Hello List,
I am trying to calculate individual genetic distances with the function `adegenet::propShared`. I found that results from `propShared` did not correlate very well with other genetic distances such as Rousset'a. Based on this results, I wrote my own function to calculate proportion of shared alleles (see below). Results from this function do not correspond with the results from `propShared`, but correlates better with other Rousset's a. Am I missing something on the methodology of `propShared`?
Thanks a lot for hints,
Best
Johannes
# --------------------------------------------------------------------------------------------------------------------------- #
# Example
# Load packages
library(adegenet)
library(stringr)
library(reshape2)
# Own function to calculate proportion shared alleles
# Following instruction from here: http://helix.biology.mcmaster.ca/brent/node8.html
psa <- function(s) {
# s - each row is a genotype, first column is id
# all combinations
idx <- combn(1:nrow(s), 2)
# calculate distances
d <- 1 - apply(idx, 2, function(x) sum(apply(s[x, -1], 2, diff) == 0)) / ncol(s[,-1])
# create object of class distance
nams <- unique(c(as.character(idx[1, ]), as.character(idx[2, ])))
dd <- structure(d, Size = length(nams), Labels = nams, Diag = FALSE, Upper = FALSE, method = "user", class = "dist")
return(dd)
}
# Example dataset
dat <- data.frame(id=as.character(1:4), x=0, y=0,
l_1=c(108, 116, 122, 119),
l_2=c(110, 114, 152, 122),
m_1=c(110, 90, 122, 69),
m_2=c(110, 111, 128, 128))
# Create genind
coords <- dat[, 2:3]
datMelted <- melt(dat[, c(1, 4:ncol(dat))])
names(datMelted) <- c("ind", "loci", "allele")
# removing 1 and 2, since it is the same loci
datMelted$loci <- str_sub(as.character(datMelted$loci), end=-3)
# Creating a genind object for the adegenet package
datCasted <- dcast(datMelted, ind ~ loci, paste, collapse="/")
gi <- df2genind(datCasted[, 2:ncol(datCasted)], sep="/", missing="NA", ind=datCasted[, 1])
# calcualte proportion of shared alleles
propShared(gi)
as.matrix(psa(dat[, -c(2,3)]))
# It is my understanding that propShared does not calcualte 1 - porpShared and is the reason for a systematic difference
# However, ind 3 and 4 differ by one of four alleles (= 0.25), but propShared suggests 0.5
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