R/methods-dimnames.R

In CoreGx: Classes and Functions to Serve as the Basis for Other 'Gx' Packages

# ==== LongTable Class

#' Get the column names from a `LongTable` object.
#'
#' @examples
#' head(colnames(merckLongTable))
#'
#' @describeIn LongTable Retrieve the pseudo-colnames of a LongTable object,
#'   these are constructed by pasting together the colIDs(longTable) and
#'   can be used in the subset method for regex based queries.
#'
#' @param x A [`LongTable`] object to get the column names from
#'
#' @return [`character`] Vector of column names.
#'
#' @export
setMethod('colnames', signature(x='LongTable'), function(x) {
    return(x@colData$.colnames)
})

#' Get the row names from a `LongTable` object.
#'
#' @examples
#' head(rownames(merckLongTable))
#'
#' @describeIn LongTable Retrieve the pseudo-rownames of a LongTable object,
#'   these are constructed by pasting together the rowIDs(longTable) and
#'   can be used in the subset method for regex based queries.
#'
#' @param x A [`LongTable`] object to get the row names from
#'
#' @return [`character`] Vector of row names.
#'
#' @export
setMethod('rownames', signature(x='LongTable'), function(x) {
    return(x@rowData$.rownames)
})

#' Getter for the dimnames of a `LongTable` object
#'
#' @examples
#' lapply(dimnames(merckLongTable), head)
#'
#' @describeIn LongTable Get the pseudo-dimnames for a LongTable object. See
#'   colnames and rownames for more information.
#'
#' @param x The [`LongTable`] object to retrieve the dimnames for.
#'
#' @return [`list`] List with two character vectors, one for row and one for
#'     column names.
#'
#' @importMethodsFrom Biobase dimnames
#' @export
setMethod('dimnames', signature(x='LongTable'), function(x) {
    return(list(rownames(x), colnames(x)))
})