Multidimentional Scaling using PLINK

Question

[User000]

Hello,

I have discovered PLINK recently and am trying to perform a multi-dimentional scaling analysis on it. I have 17 different groups with various consensus with SNP. I have created this .mds file, which looks like this,

 FID                  IID    SOL           C1           C2           C3           C4
  10_PEmerged   10_PEmerged      0    -0.161157    0.0135065    0.0558897   -0.0450944
  11_PEmerged   11_PEmerged      0   -0.0867847    0.0765844    0.0871901    0.0144553
  12_PEmerged   12_PEmerged      0    -0.197321    0.0148021   -0.0587247     0.007362

I need to plot this data, so I use the following command lines in R,

m <- as.matrix(read.table("plink.mds", header=T) )
mds <- cmdscale(as.dist(1-m))
plot(mds)

This isn't giving me the plot. Am I missing some other data file with my individuals? I was wondering if I need an additional file containing all my individuals and their phenotypes? Any tip is appreciated!

[russhh]

You might need to do

m <- read.table('plink.mds', header = TRUE)
m <- as.matrix(m[, 4:7])