fix

R/DataClasses.R

@@ -1467,6 +1467,8 @@ setClass("PeakGroupsParam",
              else TRUE
          })
 
+#' @slot rtMap,nChrompeaks slots that should not be accessed by the user.
+#' @rdname adjustRtime
 setClass("LamaParama",
          slots = c(lamas = "matrix",
                    method = "character",

R/do_adjustRtime-functions.R

@@ -759,7 +759,7 @@ adjustRtimeSubset <- function(rtraw, rtadj, subset,
 #'
 #' @author Philippine Louail, Carl Brunius
 #'
-#' @rdname matchLamaChromPeaks
+#' @rdname adjustRtime
 matchLamasChromPeaks <- function(object, param, BPPARAM = bpparam()){
     if (!hasChromPeaks(object))
         stop("'object' needs to have detected ChromPeaks. ",
@@ -796,7 +796,7 @@ matchLamasChromPeaks <- function(object, param, BPPARAM = bpparam()){
 #'
 #' @author Philippine Louail, Carl Brunius
 #'
-#' @rdname matchLamaChromPeaks
+#' @rdname adjustRtime
 summarizeLamaMatch <- function(param){
     if (!inherits(param, "LamaParama"))
         stop("The input needs to be of class 'LamaParama'")

R/functions-Params.R

@@ -312,7 +312,7 @@ LamaParama <- function(lamas = matrix(ncol = 2, nrow = 0,
 #' Function to access rtMap from `LamaParama` object
 #' @export
 #'
-#' @rdname matchLamaChromPeaks
+#' @rdname adjustRtime
 rtMap <- function(param){
     if(!inherits(param, "LamaParama"))
         stop("The inputs need to be of class LamaParama")

R/methods-Params.R

@@ -1266,7 +1266,7 @@ setReplaceMethod("subsetAdjust", "PeakGroupsParam", function(object, value) {
 #'
 #' @export
 #'
-#' @rdname matchLamaChromPeaks
+#' @noRd
 setMethod("plot", "LamaParama", function(x, index = 1L, colPoints = "#00000060",
                                          colFit = "#00000080",
                                          xlab = "Matched Chromatographic peaks",