Thresholding

After calling p-values for interactions in each of several replicates, we want to find a way to combine this information across all replicates to identify condition-specific interactions. lib5c provides a simple implementation of such a procedure.

Conceptual background

We assume each replicate belongs to one of exactly two conditions, call them “A” and “B”. This implies that there are three important classes of interactions we wish to recover:

  • “A-only” (looping in condition A but not in condition B)

  • “B-only” (looping in condition B but not in condition A)

  • “constitutive” (looping in both conditions)

We will also recover a “background” class, which will be convenient when assessing enrichments.

Command-line interface

To perform the simple two-way thresholding, run

$ lib5c threshold

Exposed functionality

The subpackage for thresholding is lib5c.algorithms.thresholding.

The main exposed function is lib5c.algorithms.thresholding.two_way_thresholding().

The following functions are exposed to compute various useful metrics from the results of two_way_thresholding():