[R] Running BayesFst in R

[jazjanes]

Hi All,

I am trying to plot outlier loci in R from data generated by BayesFst.  The
developers provide the code which I use but I can't seem to get it to work
consistently. Sometimes I can get R to generate a plot (without confidence
intervals or loci IDs) and other times I cannot even generate P-values using
the code supplied.

I am wondering if any one has used R to plot the BayesFst results and can
assist me in working out where I go wrong? Typically, R will become
unresponsive or it will provide errors at the getpvals/getfsts stages
referring to "object m1 not found" - but other times it will work. I am
uncertain exactly what m refers to, but 1440 is the # of loci and 2 is the #
of populations. M may refer to # samples??

The code is as follows:
data.matrix(read.table("fst.out")
getpvals(m1,1440,2)
getfsts(m1,1440,2)
plot(pvals[,3],pvals[,1],xlab="transformed p-values",ylab="FST")
... the code continues

Thanks


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