Changes

SeqShop: Estimates of Genetic Ancestry Practical, June 2014 (view source)

669 bytes added , 17:25, 18 June 2014

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Step 2: Combine results

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Results from previous step will be output to two files "hapmap_trios.1-3.SeqPC.coord" and "hapmap_trios.4-6.SeqPC.coord".

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Here we simply concatenate the two files while skipping the header line of the second file.

cp hapmap_trios.1-3.SeqPC.coord hapmap_trios.SeqPC.coord

more +2 hapmap_trios.4-6.SeqPC.coord >> hapmap_trios.SeqPC.coord

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Step 3: Plot results using R

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Example R codes are available in ./LASER-2.01/plot/. Let's first copy the folder to current working directory:

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cp -r ./LASER-2.01/plot/ ./

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And then we enter the directory and run the script to plot results:

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cd ./plot

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Rscript ./LASER-2.01/plot/plotHGDP.r $HGDP/HGDP_938.RefPC.coord hapmap_trios.SeqPC.coord

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A figure named "Results_on_HGDP.pdf" will be generated.

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Visualize the figure:

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evince Results_on_HGDP.pdf &

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