DAVIDsearch: Get functional annotation charts of gene lists using DAVID.

In BACA: Bubble Chart to Compare Biological Annotations by using DAVID

Description

Uploads multiple gene lists to DAVID, then perform an automated enrichment analysis based on a given database/resource (i.e., GO terms, KEGG, etc.) for each gene list. Returns DAVIDFunctionalAnnotationChart objects, one for each gene list. Requires a DAVID user id first http://david.abcc.ncifcrf.gov/webservice/register.htm. Among the optional input paramters, can use the easeScore (or P-value) to do thresholding on results. However, we suggest to get DAVID to return all possible annotations despite non-significant P-values (easeScore = 1) and perform your own thresholding when using the plot functions.

Usage

DAVIDsearch(gene.lists, david.user, idType = "AFFYMETRIX_3PRIME_IVT_ID", 
			listType = "Gene", easeScore = 1, annotation = "KEGG_PATHWAY", 
			species = NA)

Arguments

gene.lists	(Required). Lists of character vectors representing the gene lists. To compare the enrichment of differential genes specify for each list the up- and down- regulated genes, separately.
david.user	(Required). Character vector to specify the email of a given registered DAVID; it is necessary to use the DAVID web service.
idType	(Optional). Character with the type of submitted ids. Default value is "AFFYMETRIX_3PRIME_IVT_ID".
listType	(Optional). Character with the type of list (Gene, Background). Default value is "Gene".
easeScore	(Optional). Numeric with the EASE score. Default value is 1 (see DAVID Help page).
annotation	(Optional). Character vector with the category name to use in the functional annotation analysis. Default value is "KEGG_PATHWAY".
species	(Optional). Character vector with the species to use. Default value is NA. This means that DAVID will use the specie found for the submitted gene list.

Details

The following information are printed out during the the querying process: For the list "name.list" you have: - Number of genes loaded = #. - Number of genes mapped/annotated in DAVID <inDavid> = #. - Number of unmapped genes <unmappedIds> = #. - Species involved.

Value

List of DAVIDFunctionalAnnotationChart objects, one for each specified list of genes.

Author(s)

Vittorio Fortino

See Also

BBplot Jplot

Examples

  #data(gene.lists.ex)
  #result.kegg <- DAVIDsearch(gene.lists.ex, david.user = "[e-mail]") 

BACA documentation built on May 2, 2019, 7:41 a.m.