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 1.12.8 Index]