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 regular expression describing the results files from the previous step. Note that the file ending is assumed to be .csv and is automatically added.
• outfile is the filename of the merged results.

Merging Association Results

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.