Configuration file

The format of configuration file which is one of the inputs for xpore-diffmod is YAML.

Only the data and out sections are required, other sections are optional. Below is the detail for each section.

data:
    <CONDITION_NAME_1>:
        <REP1>: <DIR_PATH_TO_DATA_JSON>
        ...

    <CONDITION_NAME_2>:
        <REP1>: <DIR_PATH_TO_DATA_JSON>
        ...

    ...

out: <DIR_PATH_FOR_OUTPUTS>

criteria:
    readcount_min: <15>
    readcount_max: <1000>

method:
    # To speed up xpore-diffmod, you can use a statistical test (currently only t-test is implemented) can be used
    # to remove positions that are unlikely to be differentially modified. So, xpore-diffmod will model only
    # those significant positions by the statistical test -- usually the P_VALUE_THRESHOLD very high e.g. 0.1.
    # If you want xPore to test every genomic/transcriptomic position, please remove this prefiltering section.
    prefiltering:
        method: t-test
        threshold: <P_VALUE_THRESHOLD>

    # Here are the parameters for Bayesian inference. The default values shown in <> are used, if not specified.
    max_iters: <500>
    stopping_criteria: <0.00001>