testEnrichmentGene {sesame} | R Documentation

## testEnrichmentGene tests for the enrichment of set of probes (querySet) in gene regions.

### Description

testEnrichmentGene tests for the enrichment of set of probes (querySet) in gene regions.

### Usage

    testEnrichmentGene(querySet, databaseSets = NA, platform = NA, verbose = FALSE)

### Arguments

`querySet` | Vector of probes of interest (e.g., probes belonging to a given platform)
`databaseSets` | List of vectors corresponding to the database sets of interest with associated meta data as an attribute to each element. Optional. (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 querySet (Default: NA)
`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)
    MM285.tissueSignature = sesameDataGet('MM285.141.SE.tissueSignature')
    df = rowData(MM285.tissueSignature)
    querySet = df$Probe_ID[df$branch == "E-Brain"]
    testEnrichmentGene(querySet, platform="MM285", 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]