R/DAVIDdemo-functionalAnnotationChart.R

#' DAVID's website Functional Annotation Chart example files
#' 
#' These datasets correspond to the reports obtained using Functional
#' Annotation Chart Reports 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 GOTERM_BP_ALL,
#' GOTERM_MF_ALL and GOTERM_CC_ALL categories.
#' 
#' @format funChart1/2 are data.frame for demoList1/2 input ids,
#' respectively, with the following columns.
#' \describe{
#'  \item{Category}{factor with the main categories under used in the present
#'  analysis.}
#'  \item{Term}{character with the name of the term in format id~name (if
#'  available).}
#'  \item{Count}{integer with the number of ids of the gene list that belong to
#'  this term.}
#'  \item{X.}{after converting user input gene IDs to  corresponding DAVID gene
#'  ID, it refers to the percentage of DAVID genes in the list assoicated with
#'  particular annotation term. Since DAVID gene ID is unique per gene, it is
#'  more accurate to use DAVID ID percentage to present the gene-annotation
#'  association by removing any redundency in user gene list, i.e. two user IDs
#'  represent same gene.}
#'  \item{PValue}{numeric with the EASE Score of the term (see DAVID Help
#'  page).}
#'  \item{Genes}{character in comma separated style with the genes present in
#'  the term.}
#'  \item{List.Total, Pop.Hits, Pop.Total}{integers (in addition to Count) to
#'  build the 2x2 contingency table in order to compute the EASE Score (see
#'  DAVID Help page).}
#'  \item{Fold.Enrichment}{numeric with the ratio of the two proportions. For
#'  example, if 40/400 (i.e. 10\%) of your input genes involved in "kinase
#'  activity" and the background information is 300/30000 genes (i.e. 1\%)
#'  associating with "kinase activity", roughly 10\%/1\%=10 fold enrichment.}
#'  \item{Bonferroni, Benjamini, FDR}{numerics with p-value adjust different
#'  criterias (see p.adjust)}
#'  }
#'
#' @references 
#' \enumerate{
#'  \item The Database for Annotation, Visualization and Integrated Discovery 
#'  (\url{david.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#E3}
#' }
#'
#' @source At DAVID's website -> Start Analysis -> Demolist1/2 then go to
#' Functional Annotation Chart to obtain the appropriate reports.
#' \url{david.abcc.ncifcrf.gov}
#'
#' @author Cristobal Fresno and Elmer A Fernandez
#'
#' @docType data
#' @name funChart1
#' @rdname DAVIDdemo-functionalAnnotationChart
#' @usage data(funChart1)
#' @keywords datasets
#' @family DAVIDFunctionalAnnotationChart DataExamples
NULL
#' @name funChart2
#' @rdname DAVIDdemo-functionalAnnotationChart
#' @usage data(funChart2)
NULL
Bioconductor-mirror/RDAVIDWebService documentation built on May 31, 2017, 10:42 p.m.