Genesets-enrichr: List and download gene sets from enrichr database

In MIGSA: Massive and Integrative Gene Set Analysis

Description

enrichrGeneSets lists the database names present at enrichr. downloadEnrichrGeneSets creates a list of GeneSetCollection objects downloading the specified ones from enrichr website (https://amp.pharm.mssm.edu/Enrichr/).

Usage

`Genesets-enrichr`(pattern)

enrichrGeneSets(pattern = ".*")

## S4 method for signature 'ANY'
enrichrGeneSets(pattern = ".*")

downloadEnrichrGeneSets(geneSetNames, ...)

## S4 method for signature 'character'
downloadEnrichrGeneSets(geneSetNames, deleteMultipleEntrez = !FALSE)

Arguments

pattern	character indicating a pattern to filter the database names.
geneSetNames	list of characters with the names of the gene sets to download. Must be listed at enrichrGeneSets.
...	not in use.
deleteMultipleEntrez	logical indicating if multiple Entrez IDs should be deleted or repeated. Note: Enrichr uses Gene Symbol, if org.Hs.eg translates it into several Entrez IDs then if deleteMultipleEntrez == FALSE all Entrez are removed else all are included.

Value

enrichrGeneSets: character with present database names. downloadEnrichrGeneSets: list of GeneSetCollection objects (Genes are with their EntrezGene ID).

See Also

as.Genesets

geneSetsFromFile

loadGo

Examples

## Lets list all the gene sets that can be downloaded from Enichr website.
enrichrGeneSets()
## Not run: 
## Now lets list only the gene sets that have BioCarta in their names
## (different BioCarta versions).
enrichrGeneSets("BioCarta")

## And lets download the latest BioCarta gene sets from Enrichr.
## Make sure you use the same names as listed with enrichrGeneSets() .
biocartaGSs <- downloadEnrichrGeneSets(c("BioCarta_2015"))

## End(Not run)

MIGSA documentation built on Nov. 8, 2020, 8:26 p.m.