Nothing
# This file contains no code, it just serves to hold roxygen documentation comments
# for the package and data files so that we can do away with all Rd files
#' @title STATegRa
#' @name STATegRa
#' @aliases STATegRa-package
#' @docType package
#' @description
#' STATegRa is a package for the integrative analysis of multi-omic data-sets.
#'
#' For full information, see the user's guide.
#' @seealso \code{\link{STATegRaUsersGuide}}
NULL
#' @title STATegRa data
#' @name STATegRa_data
#' @aliases Block1 Block2 ed mapdata Block1.PCA Block2.PCA ed.PCA
#' @docType data
#' @format Two matrices with mRNA and miRNA expression data, a design matrix that describes both and a mapping between miRNA and genes.
#' @description
#' mRNA data (\code{Block1}), miRNA data (\code{Block2}) and the design matrix (\code{ed}), from \code{STATegRa_S1}, provides selected data downloaded from \url{https://tcga-data.nci.nih.gov/docs/publications/gbm_exp/}. The mapping between miRNA and mRNA (\code{mapdata}, available in \code{STATegRa_S2}) contains, as a processed matrix, selected information available from TargetScan; we selected the set of miRNA target predictions for humans for those miRNA-mRNA pairs where both miRNA and mRNA were in \code{Block1} and \code{Block2} respectively.
#'
#' The PCA version of the data (\code{Block1.PCA}, \code{Block2.PCA}, \code{ed.PCA}; available in \code{STATegRa_S3}), provides a similar data-set to \code{Block1}, \code{Block2} and \code{ed} data; however in this case the data has been processed in order to provide a pedagogic example of OmicsPCA. Results obtained from OmicsPCA (\code{\link{omicsCompAnalysis}}) with the existing data should not be taken as clinically valid.
#'
#' @source
#' (a) See \url{https://tcga-data.nci.nih.gov/docs/publications/gbm_exp/}.
#' (b) Gabor Csardi, \code{targetscan.Hs.eg.db}: TargetScan miRNA target predictions for human. R package version 0.6.1
#'
#' @author David Gomez-Cabrero, Patricia Sebastian-Leon, Gordon Ball
#' @examples
#' data(STATegRa_S1)
#' data(STATegRa_S2)
#' data(STATegRa_S3)
NULL
#' @title STATegRa data
#' @name STATegRa_data_TCGA_BRCA
#' @aliases TCGA_BRCA_Data
#' @docType data
#' @format One list, which contains three ExpressionSet objects.
#' @description
#'
#' Data were downloaded from TCGA data portal, \url{https://tcga-data.nci.nih.gov/tcga/}.
#' We downloaded sixteen tumour samples and the sixteen matching normal, for Breast invasive carcinoma, BRCA, batch 93.
#' Herein, three types of data modalities are included, RNAseq (\code{TCGA_BRCA_Data$RNAseq}), RNAseqV2 (\code{TCGA_BRCA_Data$RNAseqV2})
#' and Expression-Genes (\code{TCGA_BRCA_Data$Microarray}). The Data Level was set to Level 3.
#' For each data type, we pooled all data to one matrix, where rows corresponded to genes and columns to samples.
#' Only the first 100 genes are included.
#'
#' @source
#' See \url{https://tcga-data.nci.nih.gov/tcga/}.
#'
#' @author Nestoras Karathanasis, Vincenzo Lagani
#' @examples
#' # load data
#' data(TCGA_BRCA_Batch_93)
NULL
#' @name STATegRa-defunct
#' @title Defunct functions in STATegRa
#' @description
#' These functions have are defunct and no longer available
#' @details
#' \itemize{
#' \item{holistOmics: replaced by \code{\link{omicsNPC}}}
#' }
NULL
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.