testEnrichmentGene {sesame} | R Documentation |
testEnrichmentGene tests for the enrichment of set of probes (querySet) in gene regions.
testEnrichmentGene(querySet, databaseSets = NA, platform = NA, verbose = FALSE)
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) |
One list containing features corresponding the test estimate, p-value, and type of test.
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()