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 infiles.startTrait_*.csv from the previous step.
• outfile.csv is the filename of the merged results.

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.