getDatabaseSetOverlap {sesame}R Documentation

getDatabaseSetOverlap tests for the overlap of set of probes (querySet) in a single given feature (database set)

Description

getDatabaseSetOverlap tests for the overlap of set of probes (querySet) in a single given feature (database set)

Usage

getDatabaseSetOverlap(querySet, databaseSets, platform = NA, verbose = TRUE)

Arguments

querySet

Vector of probes corresponding to a single database set of interest.

databaseSets

List of vectors corresponding to the database sets of interest with associated meta data as an attribute to each element.

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).

verbose

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

Value

A sparse data.frame containing all of the meta data from all database sets.

Examples

library(SummarizedExperiment)
MM285.tissueSignature = sesameDataGet('MM285.tissueSignature')
df = rowData(MM285.tissueSignature)
querySet = df$Probe_ID[df$branch == "E-Brain"]
databaseSetNames = c('KYCG.MM285.seqContextN.20210630', 
'KYCG.MM285.designGroup.20210210')
databaseSets = do.call(c, lapply(databaseSetNames, sesameDataGet))
getDatabaseSetOverlap(querySet, databaseSets)


[Package sesame version 1.12.5 Index]