testEnrichmentSEA: uses the GSEA-like test to estimate the association of a...

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

uses the GSEA-like test to estimate the association of a categorical variable against a continuous variable.

Description

estimate represent enrichment score and negative estimate indicate a test for depletion

Usage

testEnrichmentSEA(
  query,
  databases,
  platform = NULL,
  silent = FALSE,
  precise = FALSE,
  prepPlot = FALSE
)

Arguments

query	query, if numerical, expect categorical database, if categorical expect numerical database
databases	database, numerical or categorical, but needs to be different from query
platform	EPIC, MM285, ..., infer if not given
silent	suppress message (default: FALSE)
precise	whether to compute precise p-value (up to numerical limit) of interest.
prepPlot	return the raw enrichment scores and presence vectors for plotting

Value

A DataFrame with the estimate/statistic, p-value, and name of test for the given results.

Examples

query <- KYCG_getDBs("KYCG.MM285.designGroup")[["TSS"]]
res <- testEnrichmentSEA(query, "MM285.seqContextN")

zwdzwd/sesame documentation built on April 28, 2024, 12:48 p.m.