R/DAVIDdemo-annotationSummary.R

In RDAVIDWebService: An R Package for retrieving data from DAVID into R objects using Web Services API.

#' DAVID's website annotation summary example files
#' 
#' These datasets correspond to the unfolded main summary categories data
#' obtained in the Annotation Summary Results page in the Database for
#' Annotation, Visualization and Integrated Discovery (DAVID) website, using as
#' input file, the ones provided for demo purposes (demoList1 or demoList2) with
#' default options. No statistical analysis is performed on these results.
#' 
#' @format annotationSummary1/2 are data.frame for demoList1/2 input ids,
#' respectively, with the following columns.
#' \describe{
#' \item{Main.Category}{factor with the main categories used in the
#' present analysis.}
#' \item{ID}{integer to identify the annotation category.} 
#' \item{Name}{character with the name of category (the ones available in
#' getAllAnnotationCategoryNames function).}
#' \item{X.}{numeric with the percentage of the gene list ids present in the
#' term.}
#' \item{Count}{integer with the number of ids of the gene list that belong to
#' this term.}
#'  }
#'
#' @references 
#' \enumerate{
#'  \item The Database for Annotation, Visualization and Integrated Discovery 
#'  (\url{davidgeneList.abcc.ncifcrf.gov})
#'  \item Huang, D. W.; Sherman, B. T.; Tan, Q.; Kir, J.; Liu, D.; Bryant, D.; 
#'  Guo, Y.; Stephens, R.; Baseler, M. W.; Lane, H. C.; Lempicki, R. A. DAVID
#'  Bioinformatics Resources: expanded annotation database and novel algorithms
#'  to better extract biology from large gene lists. Nucleic Acids Res,
#'  Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc.,
#'  National Cancer Institute at Frederick, MD 21702, USA., 2007, 35, W169-W175
#'  \item DAVID Help page
#'  \url{http://david.abcc.ncifcrf.gov/helps/functional_annotation.html#summary}
#' }
#'
#' @source At DAVID's website -> Start Analysis -> Demolist1/2 then go to
#' Show Gene List to obtain the appropriate reports. 
#' \url{david.abcc.ncifcrf.gov}
#'
#' @author Cristobal Fresno and Elmer A Fernandez
#'
#' @docType data
#' @name annotationSummary1
#' @rdname DAVIDdemo-annotationSummary
#' @usage data(annotationSummary1)
#' @keywords datasets
#' @family DataExamples
NULL
#' @name annotationSummary2
#' @rdname DAVIDdemo-annotationSummary
#' @usage data(annotationSummary2)
NULL