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#' wrapper to extract useful functions, depending if the object is
#' an ExpressionSet or a SummarizedExperiment.
#'
#' This returns an error is \code{x} is not of the correct class.
#' The package \code{SummarizedExperiment} should be available if \code{x} is of class \code{SummarizedExperiment}.
#' @param x object
#' @return if the object is an ExpressionSet or a SummarizedExperiment,
#' returns a list with the functions specific of the class of \code{x},
#' and equivalent of the ExpressionSet functions: 'sampleNames', 'featureNames',
#' 'fData', 'pData', 'exprs'
#' \itemize{
#' \item{sampleNames: }{sample names}
#' \item{featureNames: }{feature names}
#' \item{fData: }{feature annotation}
#' \item{pData: }{sample annotation}
#' \item{exprs: }{data matrix}
#' \item{varLabels: }{sample annotation variables}
#' \item{fvarLabels: }{feature annotation variables}
#' }
#' @author Laure Cougnaud
#' @import Biobase
getMethodsInputObjectEsetVis <- function(x){
if(inherits(x, what = c('ExpressionSet'))){
return(
list(
sampleNames = sampleNames,
featureNames = featureNames,
fData = fData,
pData = pData,
exprs = exprs,
varLabels = varLabels,
fvarLabels = fvarLabels
)
)
}else if(inherits(x, what = c('SummarizedExperiment', 'RangedSummarizedExperiment'))){
if(!requireNamespace("SummarizedExperiment", quietly = TRUE))
stop(paste("The package 'SummarizedExperiment' need to be loaded to use",
"the functionalities of esetVis in an 'SummarizedExperiment' object."))
return(
list(
sampleNames = colnames,
featureNames = rownames,
fData = rowData,
pData = colData,
exprs = assay,
varLabels = function(x) colnames(colData(x)),
fvarLabels = function(x) colnames(rowData(x))
)
)
}else stop("Input object is not of the correct class: 'ExpressionSet' or 'SummarizedExperiment'.")
}
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