R/rowCollapse.R

In Bioconductor/MatrixGenerics: S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects

#' Extract one cell from each row (column) of a matrix-like object
#'
#' Extract one cell from each row (column) of a matrix-like object.
#'
#' @include MatrixGenerics-package.R
#'
#' @export
#' @name rowCollapse
#'
#' @templateVar rowName rowCollapse
#' @templateVar colName colCollapse
#'
#' @template matrixStatsLink
#'
#' @template standardParameters
#' @template dimParameter
#' @param idxs An index \code{\link{vector}} with the position to extract.
#'   It is recycled to match the number of rows (column)
#' @template useNamesParameter
#'
#' @template returnVector
#'
#' @seealso
#' \itemize{
#' \item \code{matrixStats::\link[matrixStats:rowCollapse]{rowCollapse}()}
#'   and \code{matrixStats::\link[matrixStats:rowCollapse]{colCollapse}()}
#'   which are used when the input is a \code{matrix} or \code{numeric} vector.
#' }
#'
#' @examples
#'   mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
#'   mat[2, 1] <- NA
#'   mat[3, 3] <- Inf
#'   mat[4, 1] <- 0
#'
#'   print(mat)
#'
#'   rowCollapse(mat, idxs = 2)
#'   rowCollapse(mat, idxs = c(1,1,2,3,2))
#'
#'   colCollapse (mat, idxs = 4)
#'
#' @keywords array iteration robust univar
setGeneric("rowCollapse", function(x, idxs, rows = NULL, ..., useNames = TRUE) standardGeneric("rowCollapse"),
           signature = "x"
)

.matrixStats_rowCollapse <- function(x, idxs, rows = NULL, dim. = dim(x), ..., useNames = TRUE){
  matrixStats::rowCollapse(x, idxs = idxs, rows = rows, dim. = dim., ..., useNames = useNames)
}

#' @export
#' @rdname rowCollapse
setMethod("rowCollapse", "matrix_OR_array_OR_table_OR_numeric", .matrixStats_rowCollapse)

#' @export
#' @rdname rowCollapse
## Default method with user-friendly fallback mechanism.
setMethod("rowCollapse", "ANY", make_default_method_def("rowCollapse"))



#' @export
#' @rdname rowCollapse
setGeneric("colCollapse", function(x, idxs, cols = NULL, ..., useNames = TRUE) standardGeneric("colCollapse"),
           signature = "x"
)

.matrixStats_colCollapse <- function(x, idxs, cols = NULL, dim. = dim(x), ..., useNames = TRUE){
  matrixStats::colCollapse(x, idxs = idxs, cols = cols, dim. = dim., ..., useNames = useNames)
}

#' @export
#' @rdname rowCollapse
setMethod("colCollapse", "matrix_OR_array_OR_table_OR_numeric", .matrixStats_colCollapse)

#' @export
#' @rdname rowCollapse
## Default method with user-friendly fallback mechanism.
setMethod("colCollapse", "ANY", make_default_method_def("colCollapse"))