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Classify regions as hyper / hypo / inconclusive

Source: R/classify.R
classify_regions.Rd

Applies the BREAD decision rule to the output of posterior_summary():

  • hypermethylated if p_gt_delta >= prob_cutoff

  • hypomethylated if p_lt_neg_delta >= prob_cutoff

  • inconclusive otherwise

Usage

classify_regions(post, delta = 0.1, prob_cutoff = 0.95)

Arguments

post

Output of posterior_summary().

delta

Effect-size threshold used for the rule. Default 0.10. Stored as an attribute; does not re-evaluate the posterior probabilities (those must have been computed at this same delta upstream).

prob_cutoff

Posterior probability cutoff. Default 0.95.

Value

The input data.frame with an added classification factor column (levels: hypermethylated, hypomethylated, inconclusive). Attributes delta and prob_cutoff are updated.

Details

In the rare case that both probabilities exceed the cutoff (only possible for very low prob_cutoff), the region is assigned to whichever side has the larger posterior probability.