[R] Multidimensional Scaling with pairwise Fst
Jeffrey DaCosta
dacostaj at unlv.nevada.edu
Thu May 12 21:36:03 CEST 2005
I want to create a MDS plot with pairwise Fst values derived from a
population genetics project. My Fst values are in a tab-delimited file
(lower triangle only) that I view with Excel. When I use the cmdscale
command I get the message:
Error in cmdscale(x) : Distances must be result of dist or a square
matrix
In addition: Warning messages:
1: "^" not meaningful for factors in: Ops.factor(left, right)
2: "^" not meaningful for factors in: Ops.factor(left, right)
3: "^" not meaningful for factors in: Ops.factor(left, right)
4: "^" not meaningful for factors in: Ops.factor(left, right)
I transformed my values using the dist command, but the resulting plot
is not right.
My file of Fst values are the estimates of distance that I want to
directly use in the MDS analysis. Looking for help in making my Fst
file read in R as a distance matrix for this to work.
-Jeff DaCosta
dacostaj at unlv.nevada.edu
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