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