testEnrichmentAll {sesame}R Documentation

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

Description

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

Usage

testEnrichmentAll(
  querySet,
  databaseSets = NA,
  universeSet = NA,
  platform = NA,
  estimate.type = "ES",
  p.value.adj = FALSE,
  n.fdr = NA,
  return.meta = FALSE,
  verbose = FALSE
)

Arguments

querySet

Vector of probes of interest (e.g., significant probes)

databaseSets

List of vectors corresponding to the database sets of interest with associated meta data as an attribute to each element. Optional. (Default: NA)

universeSet

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).

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).

estimate.type

String indicating the estimate to report. (Default: "ES")

p.value.adj

Logical value indicating whether to report the adjusted p-value. (Default: FALSE).

n.fdr

Integer corresponding to the number of comparisons made. Optional. (Default: NA).

return.meta

Logical value indicating whether to return meta data columns for those database sets containing sparse meta data information.

verbose

Logical value indicating whether to display intermediate text output about the type of test. Optional. (Default: FALSE).

Value

One list containing features corresponding the test estimate, p-value, and type of test.

Examples

library(SummarizedExperiment)
databaseSetNames = c('KYCG.MM285.seqContextN.20210630', 
'KYCG.MM285.designGroup.20210210')
databaseSets = getDatabaseSets(databaseSetNames, verbose=FALSE)
MM285.tissueSignature = sesameDataGet('MM285.tissueSignature')
df = rowData(MM285.tissueSignature)
querySet = df$Probe_ID[df$branch == "E-Brain"]
testEnrichmentAll(querySet=querySet, 
databaseSets=databaseSets, verbose=FALSE)


[Package sesame version 1.11.14 Index]