MaxMIF

MaxMIF is a method for distinguishing the driver genes from the passenger genes by effective integration of 
somatic mutation data and molecular interaction data using 
Maximal Mutational Interaction Force model (MaxMIF).
The software is free. You can download it in https://sourceforge.net/projects/maxmif/files/

Instructions For Use

Unzip "MaxMIF.zip" to find the ** MaxMIF ** file.

## Requirements for installation
1. **Linux/Unix** environment
2. **C++**: C++ is one of the program languages, which is available for most operating systems. 
    If you are in UNIX/Linux, it is probably already installed.

We tested the code in Linux Mint environments.

## Running MaxMIF

    (*A*) You can run MaxMIF as follow.

            ./MaxMIF [Mutation data] [output prefix]

            ## [Mutation data]: path to tab-separated files that allow two formats. See the "Data Format Requirements" below;
            ## [output prefix]: the name of the mutation data, which would be the prefix name of the output file;

         You can try example run as follow.

            ./MaxMIF Background/AWG.example AWG

            or

            ./MaxMIF Background/AWGmutscore.example AWG


    (*B*) By default, two networks HumanNet and STRINGv10 would be used for running MaxMIF.
        If you need to run MaxMIF with other networks, you can run MaxMIF as follow.

            ./MaxMIF [Mutation data] [output prefix] [Network] [output suffix]

            ## [Mutation data] and [output prefix]: same as above.
            ## [Network]: path to tab-separated files of a new Network you want to use. 
                          Note that only Gene Entrez ID can be recognised when running MaxMIF. See the "Data Format Requirements" below;
            ## [output suffix]: the name of the Network, which would be the suffix name of the output file;

        You can try example run as follow.

            ./MaxMIF Background/AWG.example AWG Background/Network/STRINGv10 STRINGv10


    (*C*) Outputs
        Output files are generated in "Output" directory. 
        Genes are prioritized with their MaxMIF scores, and the presence of each gene in five reference cancer gene sets is indicated by Y (presence), or N (absence).

Data Format Requirements

(*A*) As for "Mutation Data", you can choose a tab-separated file that allow two formats:
    Note that only genes with Official Symbol can be recognised when running MaxMIF;
    The name of Mutation Data will be the prefix for output file names.

    The first format requirements are as follows:

    [GeneSymbol] tab [sample 1] tab [sample 2] tab … tab [sample M]
    [  Gene  A ] tab [ 0 or 1 ] tab [ 0 or 1 ] tab … tab [ 0 or 1 ]
    [  Gene  B ] tab [ 0 or 1 ] tab [ 0 or 1 ] tab … tab [ 0 or 1 ]
     ……
    [  Gene  C ] tab [ 0 or 1 ] tab [ 0 or 1 ] tab … tab [ 0 or 1 ]

    The second format requirements are as follows:

    [GeneSymbol] tab [MutationScore ]
    [ Gene  A  ] tab [mutation score]
    [ Gene  B  ] tab [mutation score]

(*B*) As for "Network", the default use both HumanNet and STRINGv10 for running MaxMIF.
    If you need to run MaxMIF with another network, you can input a new Network of tab-separated format;
    The name of the Network will be the suffix for output file names;

    The data format requirements are as follow:

    [Gene ID A] tab [Gene ID B] tab [the weight between Gene A and B]
    [Gene ID C] tab [Gene ID D] tab [the weight between Gene C and D]

(*C*) Outputs
    Output files are generated in "Output" directory. 
    Genes are prioritized with their MaxMIF scores, and the presence of each gene in five reference cancer gene sets is indicated by Y (presence), or N (absence).