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.. _configuration:
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>
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