altenrich: Alternative Enrichment Analysis

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Alternative Enrichment Analysis

Description

Alternative Enrichment Analysis

Usage

altenrich(
  object,
  pathwaydt,
  genevar = "gene",
  genesep = "[ ,;]",
  coef = default_coefs(object)[1],
  fit = fits(object)[1],
  significancevar = "p",
  significance = 0.05,
  effectsize = 0,
  n = 3,
  genes = FALSE,
  verbose = TRUE
)

Arguments

object	SummarizedExperiment
pathwaydt	data.table, e.g. read_msigdt
genevar	gene fvar
genesep	string or NULL
coef	string in coefs(object)
fit	'limma', 'lm', 'lme', 'lmer', 'wilcoxon'
significancevar	'p' or 'fdr'
significance	significance cutoff
effectsize	effectsize cutoff
n	no of detected genes required (for geneset to be examined)
genes	whether to record genes
verbose	whether to msg

Details

This is an alternative enrichent analysis implementation. It is more modular: uses four times .enrichment(VERBOSE)? as backend. But also four times slower than enrichment, so not recommended. It is retaind for testing purposes.

This alternative enrichment implementation

See Also

[enrichment()]

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.