wrapRDAVID: Gene enrichment analysis using the DAVID Database

In frankRuehle/systemsbio: Streamlined Analysis and Integration of Systems Biology Data

Description

Wrapper for gene enrichment analysis using the Database for Annotation, Visualization and Integrated Discovery (DAVID) accessed by the RDAVIDWebService

Usage

wrapRDAVID(
  genes,
  newheader = NULL,
  backgroundlist = NULL,
  newheaderBackground = NULL,
  davidAccount = NULL,
  projectfolder = "GEX/DAVID_Enrichment",
  projectname = "",
  maxDavid = 100,
  davidCat = c("GOTERM_BP_ALL", "GOTERM_MF_ALL", "GOTERM_CC_ALL", "KEGG_PATHWAY",
    "BIOCARTA", "UCSC_TFBS"),
  id.type = "ENTREZ_GENE_ID",
  id.column = "ENTREZID",
  sortcolumn = "adj.P.Val",
  sortdecreasing = FALSE,
  sortcolumn.threshold = 0.05,
  org = "Homo sapiens",
  threshold4enrich = 0.05,
  mincount = 2L
)

Arguments

genes	vector with gene names to analyse or dataframe or character with path to dataframe. Supplied dataframe needs to include a column with identifiers specified in id.column.
newheader	optional character vector with new header information for genes dataframe. Only relevant if genes is a dataframe or character string with filepath to a table with wrong or missing header. NULL otherwise.
backgroundlist	optional dataframe containing background list for enrichment analysis. If NULL, species specific background from DAVID is used instead.
newheaderBackground	optional character vector with new header information for backgroundlist dataframe.
davidAccount	email account for DAVID's Web Service connectivity or DAVIDWebService object.
projectfolder	character with directory for output files (will be generated if not exisiting).
projectname	optional character prefix for output file names.
maxDavid	(numeric) max number of top diff regulated elements used for enrichment analysis.
davidCat	character vector with DAVID categories to enrich for.
id.type	character with identifier DAVID uses to enrich for (e.g. "ENTREZ_GENE_ID" or "OFFICIAL_GENE_SYMBOL")
id.column	character with respective column name for id.type in genes.
sortcolumn	character with column name to be sorted for selecting top entries.
sortdecreasing	(boolean) drecreasing parameter for order of sortcolumn.
sortcolumn.threshold	numeric threshold for sortcolumn to be included in overepresentation analysis. If sortdecreasing=F, value < sortcolumn.threshold else value > sortcolumn.threshold
org	character with species name DAVID uses for enrichment (e.g."Homo sapiens" or "Mus musculus").
threshold4enrich	numeric p-value threshold for enrichment terms.
mincount	numeric minimum gene count in enrichment terms.

Details

Function uses genelist and optionally background gene list as input to perform enrichment analysis using the RDAVIDWebService. Registration for RDAVIDWebService is required at https://david.ncifcrf.gov/webservice/register.htm. Gene list can be supplied as character vector with ids given in id.type, as dataframe or as character string with path of data file. If a vector is given, sorting parameter will be ignored. Enrichment categories for a defined organism are defined in davidCat. If no connection to RDAVIDWebService can be established, NULL is returned.

Value

Functional annotation chart as R object. Additionally, a functional annotation chart is stored in the project folder as side effect.

Author(s)

Frank Ruehle

References

https://david.ncifcrf.gov/

frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.