Genesets-enrichr {MIGSA} | R Documentation

## List and download gene sets from enrichr database

### 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")

    ## End(Not run)

    ## 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"))

[Package MIGSA version 1.12.0 Index]