goatools.goea.algorithms.base module¶

Base class and shared context for GOEA term-scoring algorithms.

A GOEA algorithm turns the per-term gene sets of a study into one uncorrected p-value per GO term. The default, classic, scores every term independently. Algorithms that exploit the GO DAG topology (elim) instead score terms in a topology-driven order, letting the result for one term influence another.

class goatools.goea.algorithms.base.GoeaContext(goids, go2studyitems, go2popitems, study_ids, study_n, pop_n, godag, relationships, propagate_counts, calc_pvalue, log)¶

Bases: tuple

calc_pvalue¶: Alias for field number 9

go2popitems¶: Alias for field number 2

go2studyitems¶: Alias for field number 1

godag¶: Alias for field number 6

goids¶: Alias for field number 0

log¶: Alias for field number 10

pop_n¶: Alias for field number 5

propagate_counts¶: Alias for field number 8

relationships¶: Alias for field number 7

study_ids¶: Alias for field number 3

study_n¶: Alias for field number 4

class goatools.goea.algorithms.base.GoeaAlgoResult(go2pval, go2flds)¶

Bases: tuple

go2flds¶: Alias for field number 1

go2pval¶: Alias for field number 0

class goatools.goea.algorithms.base.GoeaAlgorithm[source]¶

Bases: object

Abstract base for GOEA term-scoring algorithms.

name = None¶

default_alternative = None¶

pvals_precorrected = False¶

run(ctx)[source]¶: Score ctx.goids. Returns a GoeaAlgoResult.