NAME
	PPSampler2 (Proteins' Partition Sampler Version 2) - predicts protein complexes
	from weighted protein-protein interactions 

SYNOPSIS
	PPSamplers [OPTIONS]

OPTIONS
	-f, --file
		specify a file of protein-protein interactions (PPIs) with their weights, 
        where each line should contain two protein IDs and the 
        corresponding interaction weight, which are tab-deliminated. 
	Optionally, three files of PPIs with weights for protein complexes 
        of size two, three, and four or more can be specified in the format of 
        fileOfSize2;fileOfSize3;fileOfSize4OrMore.
	-h, --help
		show help document and exit.
	--output <output>
		set an output file to be <output>. The default is "output.txt" in 
        the working directory.
	--maxClusterSize <maxClusterSize>
		set the possible maximum size of clusters to be predicted to be 
        <maxClusterSize>. The default is 100.
	--temperature <temperature>
		set the temperature parameter to be <temperature>. This parameter 
        controls acceptance rate of candidate state. The default is 1e-9.
	--gamma <gamma> 
		set the parameter, gamma, of the score subfunction, f_2, to be 
        <gamma>. The default is 2.
    --f1DenominatorExponent <exponent>
        set the exponent of the denominator of f1(c), where c is a cluster, 
        to be <exponent>. The default is 0.5. 
    --f2
        add the function, f2, into the whole scoring function, f. Without this 
        option, f2 is not included in f. In the default, this option is not valid.
    --f2variance1 <v1>
        The variance of f2 is <v1>/<v2>^(cluster size), where <v2> is specified 
        by the next option, --f2variance2. The default is 1000.
    --f2variance2 <v2>
        see the above. The default is 1.1.
	--lambda <lambda>
		set the parameter, lambda, of the score subfunction, f_3, to be 
        <lambda>. The default is 2000.
    --f3variance <variance>
        set the variance of f3 to be <variance>. The default is 1e6. 
    --maxIterationCount <maxIterationCount>
        set the repeat count to be <maxIterationCount>. The default is 
        2e6, in which case, PPSampler2 will stop in 20 minutes. 
    --proposalDitribution <proposalDitribution>
    	specify a proposal distribution. <proposalDitribution> is either 1 
        or 2. The option of 1 corresponds to the proposal distribution given in [1]. 
	The option of 2 is the modification of the former one, which is explained in [2]. 
	 This is more efficient 
	in time than the former. We recommend to use the option of 2. 
	The default is 2. 
    --beta <beta>  
        set the parameter, beta, of both proposal distribuitions. <beta> 
        should be in [0..1]. The default is 0.01.
    --noPlot
        makes no graphs of historical scores. Without this option, graphs 
        are given.
    -v, --version
        output version information and exit.

REFERENCE 

	[1] Daisuke Tatsuke and Osamu Maruyama, Sampling strategy for
	protein complex prediction using cluster size frequency, Gene,
	2012.

    	[2] Chasanah Kusumastuti Widita and Osamu Maruyama,
    	PPSampler2: Predicting Protein Complexes More Accurately and
    	Efficiently by Sampling, BMC Systems Biology, To appear.