comparison_input_file.txt

# Note: lines starting with '#' are ignored

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# Comparison type: Compare peptide nodes ('PEPTIDE_NODES') or protein nodes ('PROTEIN_NODES')
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comparison_type = PROTEIN_NODES

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# FDR threshold: only consider the entries with a FDR value greater than the threshold
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threshold = 0.05

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# INPUT FILES TO COMPARE 
# Each file contains two columns, separated by a TAB.
# first column correspond with the name of the dataset
# second column correspond with the full path to the file corresponding to the FDR output file of a PCQ analysis, which typically is named as: 'prefix_FDR_sufix.txt' where prefix and sufix correspond to the input analysis parameters: 'output_prefix' and 'output_sufix'
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dataset1 = /path_to_significance_files/prefix1_finalTable_suffix1.txt
dataset2 = /path_to_significance_files/prefix2_finalTable_suffix2.txt
dataset3 = /path_to_significance_files/prefix2_finalTable_suffix2.txt