p <- read.table("phenotypes")[,1]
plot(mds,col=p)
id <- read.table("ids")[,1]
plot(mds,type="n")
text(mds,as.character(id))
To save a plot as EPS
plot(mds)
dev.copy2eps(file="myplot.eps")
To redirect to PDF
pdf(file="myplot.pdf")
plot(mds)
dev.off()
My sample consists of sibling pairs? Can I perform a
sibling-based analysis?
The --within-file or --within options: for example,
to permute individuals only within family ID groups, use the
following:
plink --file mydata --assoc --within --family
How can I check my file prior to using PLINK?
One approach is to use Unix tools: the things to check are that every
row has the same number of items. For example,
gawk ' { print NF } ' myfile.ped | sort | uniq -c
should just give one line of output (showing the number of lines, and
the number of items each line has). More than two lines of output
indicates that the file is not properly formed.
To check pedigree structure, you might use the program PEDSTATS or
FAMTYPES.
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