Description Usage Arguments Value Examples
Uploads a gene list to DAVID, then performs a GO enrichment analysis. Requires registration with DAVID first here. Returns a DAVIDFunctionalAnnotationChart object which can be easily coerced into a data.frame. DAVID does some automatic thresholding on results. For Z-score standardisation, we found it useful to get DAVID to return all possible annotations despite non-significant P-values and perform our own thresholding.
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geneList |
Either a list of genes or a GRanges result from annotateBedFromDb to upload and functionally enrich |
david |
An RDAVIDWebService object can be passed to the function so a new one doesn't have to be requested each time |
email |
If david==NULL, an email must be supplied. DAVID requires (free) registration before users may interact with their WebService API. This can be accomplished online (here), then the registered email supplied here. |
idType |
The type of gene IDs being uploaded (MGI, Entrez,...) |
listName |
The name to give the list when it's uploaded to the WebService |
count |
Minimum number of genes per GO term |
PVal |
P-value threshold for GO terms |
background |
If you want to perform enrichment against a specific background instead DAVID's default (whole genome), supply it here |
bgIdType |
If the background gene ID type is different from the gene list, enter it here |
bgListName |
If you want to give the background a name, enter it here |
getKEGG |
TRUE if you want to download KEGG pathway information as well as GO |
Returns a DAVIDFunctionalAnnotationChart after generating it by comparing the supplied gene list to the full genome as a background
1 2 3 4 5 6 7 8 9 10 11 12 | ## not run because registration is required
## visit http://david.abcc.ncifcrf.gov/webservice/register.htm to register
## Not run:
## You can either supply the registered email:
fnAnot = getFnAnot_genome(exp1$gene_id,
email = "your.registered@email.com",
idType="ENTREZ_GENE_ID", listName="My_gene_list-1")
## Or create a DAVIDWebService object with the email:
david = DAVIDWebService$new(email = "your.registered@email.com")
fnAnot = getFnAnot_genome(entrezList, david = david)
## End(Not run)
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