R/documentation.R

In CancerInSilico: An R interface for computational modeling of tumor progression

#' CancerInSilico
#'
#' \tabular{ll}{
#' Package: \tab CancerInSilico\cr
#' Type: \tab Package\cr
#' Version: \tab 1.99.0\cr
#' Date: \tab 2017-06-24\cr
#' License: \tab LGPL\cr
#' }
#' @author Maintainer: Elana J. Fertig \email{ejfertig@jhmi.edu},
#'             Thomas D. Sherman \email{tsherma4@jhu.edu}
#' @docType package
#' @name CancerInSilico
#' @import utils
#' @importFrom Rcpp evalCpp
#' @useDynLib CancerInSilico
NULL

#' This data contains the list of gene targets of modeled signaling pathways
#' 
#' @docType data
#' @name inSilicoPathways
#' @usage inSilicoPathways
#' @details List of gene targets for GtoM, GtoS, and Growth factor pathways
#' modeled in CancerInSilico. GtoM represents genes associated with the G to M
#' checkpoint of the cell cycle collected from PID pathways PI3KCI_AKT, TNF,
#' TGFBR, and RB1 in MSigDB v5.1. GtoS represented genes associated with the 
#' G to S checkpoint of the cell cycle collected from E2F target genes in PID
#' and hallmark genesets from MSigDb v5.1 and exprimentally validated targets
#' in TRANSFAC professional 2014. Growth represents the targets of transcription
#' factors resulting from EGFR activition (STAT1, STAT3, STAT5, Elk-1, Myc,
#' NF-kappaB, and RelA) from the TRANSFAC professional database 2014 as
#' described in Fertig et al, 2012.
#' @references Subramanian, Tamayo, et al, PNAS, 102:155545, 2005; Matys et al,
#' Nuc Ac Res, 34:D108, 2006; and Fertig et al, BMC Genomics, 13:160, 2012.
#' @return List of gene targets for GtoM, GtoS, and Growth factor pathways.
#' 
NULL

#' gene expression data for genes in sample pathways
#' @docType data
#' @name referenceGeneExpression
#' @usage referenceGeneExpression
NULL

#' sample cell model
#' @docType data
#' @name modDefault
#' @usage modDefault
NULL

#' sample cell model
#' @docType data
#' @name modLargeRun
#' @usage modLargeRun
NULL

#' sample cell model
#' @docType data
#' @name modLongRun
#' @usage modLongRun
NULL

#' sample cell model
#' @docType data
#' @name modHighDensity
#' @usage modHighDensity
NULL

#' sample cell model
#' @docType data
#' @name modCellTypes
#' @usage modCellTypes
NULL

#' sample cell model
#' @docType data
#' @name modDrugs
#' @usage modDrugs
NULL

#' sample pathway
#' @docType data
#' @name pwyGrowth
#' @usage pwyGrowth
NULL

#' sample pathway
#' @docType data
#' @name pwyMitosis
#' @usage pwyMitosis
NULL

#' sample pathway
#' @docType data
#' @name pwySPhase
#' @usage pwySPhase
NULL

#' sample pathway
#' @docType data
#' @name pwyContactInhibition
#' @usage pwyContactInhibition
NULL

run_cpp_unit_tests <- function()
{
    run_catch_unit_tests()
}