[R] Multidimensional Scaling with pairwise Fst

From: Jeffrey DaCosta <dacostaj_at_unlv.nevada.edu>
Date: Fri 13 May 2005 - 05:36:03 EST


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@unlv.nevada.edu



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