submit_to_david {cola} | R Documentation |
Perform DAVID analysis
submit_to_david(genes, email, catalog = c("GOTERM_CC_FAT", "GOTERM_BP_FAT", "GOTERM_MF_FAT", "KEGG_PATHWAY"), idtype = "ENSEMBL_GENE_ID", species = "Homo sapiens")
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 |
idtype |
ID types for the input gene list. Valid values should be in |
species |
full species name if the ID type is not uniquely mapped to one single species. |
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 our 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.
A data frame with functional enrichment results.
Zuguang Gu <z.gu@dkfz.de>
# There is no example NULL