getFnAnot_genome: Get the functional annotation chart of a gene list using DAVID

Description

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.

Usage

getFnAnot_genome(geneList, david = NULL, email = NULL, idType = "ENTREZ_GENE_ID", listName = "auto_list", count = 1L, PVal = 1, background = NULL, bgIdType = NULL, bgListName = NULL, getKEGG = FALSE)

Arguments

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

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

Value

Returns a DAVIDFunctionalAnnotationChart after generating it by comparing the supplied gene list to the full genome as a background

Examples

Run this code

## 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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