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

In sam-bassett/CompGO: An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation

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
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

Value

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

Examples

## 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$gene_id,
   email = "[e-mail]",
   idType="ENTREZ_GENE_ID", listName="My_gene_list-1")
## Or create a DAVIDWebService object with the email:
david = DAVIDWebService$new(email = "[e-mail]")
fnAnot = getFnAnot_genome(entrezList, david = david)

## End(Not run)

sam-bassett/CompGO documentation built on May 29, 2019, 1:01 p.m.