Postprocessing

Postprocessing

Concatenating Files

If the association updates have been computed blockwise, we have to merge the partial results to one file:

./GNetLMM/bin/gNetLMM_postprocess --concatenate --infiles infiles --outfile outfile

• infiles is a unique prefix describing the results files from the previous step.
• outfile is the filename of the merged results.

For in- and output files, the file ending is assumed to be .csv and is automatically added.

Merging Association Results

Finally, we merge the results from the initial association scan with the updated assocations:

./GNetLMM/bin/gNetLMM_postprocess --merge_assoc --assoc0file $ASSOC0FILE --assocfile $ASSOCFILE

• assoc0file is the basename of the initial association scan.
• assocfile is the basename of the updated association scan. The updates p-values are assumed to be saved in assocfile.csv for the method to be working. P-values are saved in assocfile.pv.matrix, SNP weights in assocfile.beta.matrix.

Plotting Power

Finally, we plot the power of GNetLMM versus a vanilla LMM:

./GNetLMM/bin/gNetLMM_postprocess --plot_power --assocfile assocfile --assoc0file assoc0file  --plotfile plotfile --pfile pfile --bfile bfile --window window

• assocfile is the basename of the GNet-LMM resultsfile.
• assoc0file is the basename of the LMM resultsfile.
• plotfile is the filename of the power plot.
• bfile is the basename of the bed file.
• pfile is the basename of the phenotype matrix.
• window determines the minimal distance between the SNP and the gene to call the association a trans association.