testEnrichment: testEnrichment tests for the enrichment of set of probes...

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

testEnrichment tests for the enrichment of set of probes (query set) in a number of features (database sets).

Description

testEnrichment tests for the enrichment of set of probes (query set) in a number of features (database sets).

Usage

testEnrichment(
  query,
  databases = NULL,
  universe = NULL,
  alternative = "greater",
  include_genes = FALSE,
  platform = NULL,
  silent = FALSE
)

Arguments

query	Vector of probes of interest (e.g., significant probes)
databases	List of vectors corresponding to the database sets of interest with associated meta data as an attribute to each element. Optional. (Default: NA)
universe	Vector of probes in the universe set containing all of the probes to be considered in the test. If it is not provided, it will be inferred from the provided platform. (Default: NA).
alternative	"two.sided", "greater", or "less"
include_genes	include gene link enrichment testing
platform	String corresponding to the type of platform to use. Either MM285, EPIC, HM450, or HM27. If it is not provided, it will be inferred from the query set probeIDs (Default: NA).
silent	output message? (Default: FALSE)

Value

A data frame containing features corresponding to the test estimate, p-value, and type of test.

Examples

library(SummarizedExperiment)
df <- rowData(sesameDataGet('MM285.tissueSignature'))
query <- df$Probe_ID[df$branch == "B_cell"]
res <- testEnrichment(query, "chromHMM", platform="MM285")
sesameDataGet_resetEnv()

zwdzwd/sesame documentation built on Nov. 11, 2024, 9:33 a.m.