Add rng_seed parameter for reproducibility; document n_null and win_exp guidance - #16
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Add rng_seed parameter for reproducibility; document n_null and win_exp guidance#16jordiabante with Copilot wants to merge 4 commits into
rng_seed parameter for reproducibility; document n_null and win_exp guidance#16jordiabante with Copilot wants to merge 4 commits into
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[WIP] Address questions on cpel pipeline parameters
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rng_seed parameter for reproducibility; document n_null and win_exp guidance
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Users raised three questions about pipeline parameter tuning: appropriate
n_nulliteration counts, how to choosewin_exp, and the absence of a fixed random seed for reproducibility.Changes
rng_seedparameter — new optional keyword argument (default: -1, no seeding) on bothcomp_tnullandrun_analysis. When set to a non-negative integer, seeds the main-process RNG and each distributed worker independently (rng_seed + wid) to prevent identical streams across parallel workers:n_nulldocumentation — docstrings now note that 10,000 iterations produce a more accurate null distribution and enable detection of all three signal types (MML, NME, PDM); the default of 1,000 may miss MML/PDM signals.win_expdocumentation — docstring now notes that larger values (150–250 bp) capture more reads and CpG sites at the cost of potentially spanning additional variants, and recommends aligning the value with the sequencing read length.Warning
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