Good evening,
I have been using R (ade4) and amova() to analyze my RAPD data from plants.
Creating the adequate $distance and $structure df works fine. However I have a
problem creating the $sample df from my original data.
My data set looks something like this:
region <- rep(c("east","west"),each=8)
pop <- c(rep(1:4,each=4))
ind <- c(rep(1:4,4))
l.1 <- c(1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0)
l.2 <- sample(c(0,1),16,replace=T)
l.3 <- sample(c(0,1),16,replace=T)
l.4 <- sample(c(0,1),16,replace=T)
l.5 <- sample(c(0,1),16,replace=T)
l.6 <- sample(c(0,1),16,replace=T)
data <- data.frame(region,pop,ind,l.1,l.2,l.3,l.4,l.5,l.6)
data
Creating the $samples df works fine that way
pop <- as.factor(pop)
samples <- as.data.frame(model.matrix(~-1 + pop))
names(samples) <- levels(pop)
But if I subset my original dataset:
data.short <- data[data$pop %in% c(1:3),]
data.short
and try to create the $samples again I still get the original $samples output.
pop <- as.factor(pop)
samples <- as.data.frame(model.matrix(~-1 + pop))
names(samples) <- levels(pop)
Any ideas how I can solve this? Additionally, how can I erase duplicate
genotypes and note double presence in the $samples df?
I am happy for any comments. Cheers
Patrick
-- Patrick Kuss PhD-student Institute of Botany University of Basel Schönbeinstr. 6 CH-4056 Basel +41 61 267 2976---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
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