david_enrichment {cola} | R Documentation

## Perform DAVID enrichment analysis

### Description

Perform DAVID enrichment analysis

### Usage

    david_enrichment(genes, email,
        catalog = c("GOTERM_CC_FAT", "GOTERM_BP_FAT", "GOTERM_MF_FAT", "KEGG_PATHWAY"),
        idtype = "ENSEMBL_GENE_ID", species = "Homo sapiens")

### Arguments

`genes` | A vector of gene identifiers.
`email` | The email that user registered on DAVID web service (https://david.ncifcrf.gov/content.jsp?file=WS.html ).
`catalog` | A vector of function catalogs. Valid values should be in `cola:::DAVID_ALL_CATALOGS`.
`idtype` | ID types for the input gene list. Valid values should be in `cola:::DAVID_ALL_ID_TYPES`.
`species` | Full species name if the ID type is not uniquely mapped to one single species.

### Details

This function directly sends the HTTP request to DAVID web service (https://david.ncifcrf.gov/content.jsp?file=WS.html ) and parses the returned XML. The reason of writing this function is I have problems with other R packages doing DAVID analysis (e.g. RDAVIDWebService, https://bioconductor.org/packages/devel/bioc/html/RDAVIDWebService.html ) because the rJava package RDAVIDWebService depends on can not be installed on my machine.

Users are encouraged to use more advanced gene set enrichment tools such as clusterProfiler (http://www.bioconductor.org/packages/release/bioc/html/clusterProfiler.html ), or fgsea (http://www.bioconductor.org/packages/release/bioc/html/fgsea.html ).

If you want to run this function multiple times, please set time intervals between runs.

### Value

A data frame with functional enrichment results.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### See Also

Now cola has a replacement function `functional_enrichment` to perform enrichment analysis.

### Examples

    # There is no example
    NULL

[Package cola version 1.8.1 Index]