testEnrichment {sesame} | R Documentation

## 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(
      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 = do.call(c, lapply(databaseSetNames, sesameDataGet))
    MM285.tissueSignature = sesameDataGet('MM285.141.SE.tissueSignature')
    df = rowData(MM285.tissueSignature)
    querySet = df$Probe_ID[df$branch == "E-Brain"]
    testEnrichment(querySet=querySet, databaseSets=databaseSets, verbose=FALSE)

    # release memory for Windows package builder
    rm(list=ls(env=sesameData:::cacheEnv), envir=sesameData:::cacheEnv)
    gc()

[Package sesame version 1.12.9 Index]