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#' fNames Generic
#'
#' A generic for the fNames method
#'
#' @examples
#' fNames(clevelandSmall_cSet, "rna")
#'
#' @param object The \code{CoreSet}
#' @param mDataType The molecular data type to return feature names for
#' @param ... Fallthrough arguements for defining new methods
#'
#' @return A \code{character} vector of the feature names
setGeneric("fNames", function(object, mDataType, ...) standardGeneric("fNames"))
#' @describeIn CoreSet Return the feature names used in the dataset
#' @export
setMethod(fNames, "CoreSet", function(object, mDataType){
if (mDataType %in% names(object@molecularProfiles)) {
rownames(featureInfo(object, mDataType))
} else {
stop(paste0("Molecular data type ", mDataType ," is not part of this ", class(object)))
}
})
#' fNames<- Generic
#'
#' A generic for the fNames replacement method
#'
#' @examples
#' data(clevelandSmall_cSet)
#' fNames(clevelandSmall_cSet, "rna") <- fNames(clevelandSmall_cSet, "rna")
#'
#' @param object The \code{CoreSet} to update
#' @param mDataType The molecular data type to update
#' @param value A \code{character} vector of the new cell names
#'
#' @return Updated \code{CoreSet}
#' @export
setGeneric("fNames<-", function(object, mDataType, value)
standardGeneric("fNames<-"))
#' @describeIn CoreSet Update the feature names used in a molecular profile
#' @export
setReplaceMethod("fNames",
signature = signature(object="CoreSet", mDataType='character',
value="character"),
function(object, mDataType, value)
{
if (mDataType %in% names(object@molecularProfiles)) {
rownames(featureInfo(object, mDataType)) <- as.character(value)
object
} else {
stop(paste0(mDataType, " is not in the object. Possible mDataTypes are: ", names(object@molecularProfiles)))
}
})
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