Question: Are Plink MDS plots supposed to complete so quickly?
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gravatar for devenvyas
24 months ago by
devenvyas340
University of Florida
devenvyas340 wrote:

I ran MDS plots on a data set of >620,000 SNPs and 934 individuals using plink.

I followed the advice of a former labmember as well as this tutorial (https://www.staff.ncl.ac.uk/heather.cordell/pak2010MDS.html - mainly just the stuff after "To perform MDS analysis in PLINK, we first calculate a file").

plink --file dataset --genome --out dataset
plink --file dataset --read-genome dataset --mds-plot $k --out "dataset_"$k

($k is looped in and is the number of MDS dimensions ranging from 1 to 20).

The first line (genome file creation) does take a while, but I have noticed that the actual mds generation takes about 10 minutes per run and uses about half a gigabyte of RAM, which seems suspiciously quick and non-intensive.

Anyone have any experience with this? (i.e., am I doing something wrong, or is this normal)

 

 

mds snp plink • 771 views
ADD COMMENTlink written 24 months ago by devenvyas340

Actually, once your data has been converted to binary, genome file creation should take less than two minutes with your dataset with PLINK 1.9 on most systems, and --mds-plot should take less than one.

ADD REPLYlink written 24 months ago by chrchang5232.3k

This was running on Plink 1.07, single threaded. HPC just got Plink 1.9 installed this morning, so I haven't tried it out yet.

ADD REPLYlink written 24 months ago by devenvyas340
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