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669 bytes added
, 17:25, 18 June 2014
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| Step 2: Combine results | | 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". |
| + | Here we simply concatenate the two files while skipping the header line of the second file. |
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| cp hapmap_trios.1-3.SeqPC.coord hapmap_trios.SeqPC.coord | | cp hapmap_trios.1-3.SeqPC.coord hapmap_trios.SeqPC.coord |
| more +2 hapmap_trios.4-6.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/ ./ |
| + | |
| + | And then we enter the directory and run the script to plot results: |
| + | cd ./plot |
| + | Rscript ./LASER-2.01/plot/plotHGDP.r $HGDP/HGDP_938.RefPC.coord hapmap_trios.SeqPC.coord |
| + | |
| + | A figure named "Results_on_HGDP.pdf" will be generated. |
| + | Visualize the figure: |
| + | |
| + | evince Results_on_HGDP.pdf & |