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A genotype imputation method based on K-nearest-neighbor and mismatch accumulator array.
There is a two step approach for the imputation method. As a fist step, testing is performed and a large number of windows is preferred to test. The best option for the actual run is to select the window with the highest estimated accuracy. More specifically, in the example data set the window that should be used for the actual permutation is window 12.
- To use NPUTE, import your data in csv format.
- Resources: NPUTEv1
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> npute. The input example data is called sample_data.csv, the testing_out.csv is the example output from the first step where we test for the optimum window. The Imputation_out.csv is the example output produced by the example data.
Use sample_data.csv from the directory above as test input.
Steps to run the App
When the app is run in the Discovery Environment, use the following steps with the above input file(s) to get the output provided in the next section below.
Steps to run the program.
1st step define optimum window
1.Select the file for the analysis
2. Under Options select testing
3.Specify window range
4.Leave "enter window size" option empty
3.Define the name of the output file under output
4.Run the testing
3.Inspect the output and choose the window with the highest estimated accuracy
2nd step run the actual permutation
1.Select the file for the analysis(should be the same as in the previous step)
2. Under Options select imputing
3.Leave "Specify window range" empty
4. In "Enter window size" box enter the window selected in the previous step
5. Under Output specify the output file name
6. Run the Imputation
Expect as an output from the first step testing_out.txt. From the second step expect as an output Imputation_out.csv file.