altenrich: Alternative Enrichment Analysis

altenrichR Documentation

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/importomics documentation built on June 15, 2024, 1:05 a.m.