Concordance Typed and Imputed SNPs

Example input files

Impute output

impute.gen
impute.sample

Plink raw output --recodeA option

plink.raw

Run

Rscript concordance.R impute.gen impute.sample plink.raw rs17599629

Output

Scatter plot PNG file - rs17599629.png.

Scatter plot data file - rs17599629_PlotFile.txt

head rs17599629_PlotFile.txt

IID Imputed Typed
Sample2501 0 0
Sample2536 0.001 0
Sample2537 0 0
Sample2538 0.997 1
Sample2539 0 0
Sample2540 0.684 1
Sample2541 0.997 1
Sample2542 0.992 1
Sample2543 1.093 1

Correlation summary for rs17599629:

• MatchingSamples - typed and imputed samples overlap.
• MatchingSamplesExclNoCall - typed and imputed samples overlap, excluding NoCalls.
• Concordance - correlation between imputed and typed SNP.

         SNP MatchingSamples MatchingSamplesExclNoCall Concordance
1 rs17599629            1267                       911   0.9223097