Genesets-enrichr {MIGSA} | R Documentation |
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/).
`Genesets-enrichr`(pattern) enrichrGeneSets(pattern = ".*") ## S4 method for signature 'ANY' enrichrGeneSets(pattern = ".*") downloadEnrichrGeneSets(geneSetNames, ...) ## S4 method for signature 'character' downloadEnrichrGeneSets(geneSetNames, deleteMultipleEntrez = !FALSE)
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 |
... |
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. |
enrichrGeneSets: character with present database names. downloadEnrichrGeneSets: list of GeneSetCollection objects (Genes are with their EntrezGene ID).
## 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)