Fixed warnings during Rd. documentation generation on M$ Windows.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pmp
 Type: Package
 Title: Peak Matrix Processing and signal batch correction for metabolomics data sets
-Version: 0.99.1
+Version: 0.99.2
 Author: Andris Jankevics and Ralf Weber
 Maintainer: Andris Jankevics <[email protected]>
 Description: Tools for scaling, normalisation and filtering of metabolomics data

R/checkPeakMatrix.R

@@ -56,15 +56,15 @@ check_peak_matrix <- function(df, classes=NULL) {
 }
 
 #' If needed convert input data to object of class 
-#' \link[SummarizedExperiment]{SummarizedExperiment}
+#' \link[SummarizedExperiment]{RangedSummarizedExperiment-class}
 #' 
 #' @param df A matrix-like (e.g. an ordinary matrix, a data frame) object with
 #' all values of class \code{numeric()} or \code{integer()} of peak
 #' intensities, areas or other quantitative characteristic.
 #' @param classes \code{character()}, vector of class labels. Must be the same 
 #' length as the number of sample in the input peak table.
 #' @return object of class of 
-#' \link[SummarizedExperiment]{SummarizedExperiment}. 
+#' \link[SummarizedExperiment]{RangedSummarizedExperiment-class}. 
 #' 
 #' @noRd
 check_input_data <- function (df, classes=NULL){
@@ -89,7 +89,7 @@ check_input_data <- function (df, classes=NULL){
 }
 
 #' If input data object was not of class of 
-#' \link[SummarizedExperiment]{SummarizedExperiment},
+#' \link[SummarizedExperiment]{RangedSummarizedExperiment-class},
 #' convert output to the original R data structure. 
 #' 
 #' All values stored in \code{metadata} element of \code{SummarizedExperiment}

R/data.R

@@ -47,7 +47,8 @@
 #' @references Kirwan et al, Scientific Data volume 1,
 #'Article number: 140012 (2014) https://www.nature.com/articles/sdata201412
 #'
-#' @format A \link[SummarizedExperiment]{SummarizedExperiment} object. \cr
+#' @format A \link[SummarizedExperiment]{RangedSummarizedExperiment-class} 
+#' object. \cr
 #' \code{assay(MTBLS79)} Peak intensities of the DIMS data set. 
 #' Contains 172 samples and 2488 features. \cr
 #' \code{colData(MTBLS79)} Sample meta data containing 4 columns. \cr

R/filters.R

@@ -18,9 +18,9 @@ NULL
 #' used to calculate the median signal intensity.
 #'
 #' @param df A matrix-like (e.g. an ordinary matrix, a data frame) or 
-#' \link[SummarizedExperiment]{SummarizedExperiment} object with all values of 
-#' class \code{numeric()} or \code{integer()} of peak intensities, areas or 
-#' other quantitative characteristic.
+#' \link[SummarizedExperiment]{RangedSummarizedExperiment-class} object with 
+#' all values of class \code{numeric()} or \code{integer()} of peak 
+#' intensities, areas or other quantitative characteristic.
 #' @param fold_change \code{numeric(1)}, fold_change minimum fold change 
 #' between analytical and blank samples.
 #' @param classes \code{character()}, vector of class labels. Must be the same 
@@ -42,9 +42,9 @@ NULL
 #' matrix-like (e.g. an ordinary matrix, a data frame) object, function returns 
 #' \code{numeric()} matrix-like object of filtered data set. Function 
 #' \code{flags} are added to the object \code{attributes} and is a 
-#' \link[S4Vectors]{DataFrame} with five columns. The same \code{DataFrame} 
-#' object containing flags is added to \code{rowData()} element of 
-#' \code{SummarizedExperiment} object as well.\cr
+#' \link[S4Vectors]{DataFrame-class} with five columns. The same 
+#' \code{DataFrame} object containing flags is added to \code{rowData()} 
+#' element of \code{SummarizedExperiment} object as well.\cr
 #' \cr
 #' Columns in \code{rowData()} or \code{flags} element contain: \cr
 #' \code{median_non_blanks} median intensities of features of non-blank
@@ -130,9 +130,9 @@ filter_peaks_by_blank <- function(df, fold_change, classes, blank_label,
 #' matrix-like (e.g. an ordinary matrix, a data frame) object, function returns 
 #' \code{numeric()} matrix-like object of filtered data set. Function 
 #' \code{flags} are added to the object \code{attributes} and is a 
-#' \link[S4Vectors]{DataFrame} with five columns. The same \code{DataFrame} 
-#' object containing flags is added to \code{rowData()} element of 
-#' \code{SummarizedExperiment} object as well.\cr
+#' \link[S4Vectors]{DataFrame-class} with five columns. The same 
+#' \code{DataFrame} object containing flags is added to \code{rowData()} 
+#' element of \code{SummarizedExperiment} object as well.\cr
 #' \cr
 #' 
 #' Columns in \code{rowData()} or \code{flags} element contain \code{fractions} 
@@ -257,9 +257,9 @@ remove_peaks <- function(df, rem_index) {
 #' matrix-like (e.g. an ordinary matrix, a data frame) object, function returns 
 #' \code{numeric()} matrix-like object of filtered data set. Function 
 #' \code{flags} are added to the object \code{attributes} and is a 
-#' \link[S4Vectors]{DataFrame} with five columns. The same \code{DataFrame} 
-#' object containing flags is added to \code{rowData()} element of 
-#' \code{SummarizedExperiment} object as well.\cr
+#' \link[S4Vectors]{DataFrame-class} with five columns. The same 
+#' \code{DataFrame-class} object containing flags is added to \code{rowData()} 
+#' element of \code{SummarizedExperiment} object as well.\cr
 #' \cr
 #' Columns in \code{rowData()} or \code{flags} element contain: \cr
 #' \code{rsd_QC} \code{numeric()}, RSD\% value of QC samples per feature; \cr
@@ -311,9 +311,9 @@ filter_peaks_by_rsd <- function(df, max_rsd, classes, qc_label,
 #' matrix-like (e.g. an ordinary matrix, a data frame) object, function returns 
 #' \code{numeric()} matrix-like object of filtered data set. Function 
 #' \code{flags} are added to the object \code{attributes} and is a 
-#' \link[S4Vectors]{DataFrame} with five columns. The same \code{DataFrame} 
-#' object containing flags is added to \code{rowData()} element of 
-#' \code{SummarizedExperiment} object as well. If element 
+#' \link[S4Vectors]{DataFrame-class} with five columns. The same 
+#' \code{DataFrame} object containing flags is added to \code{rowData()} 
+#' element of \code{SummarizedExperiment} object as well. If element 
 #' \code{colData()} already exists flags are appended to existing values.\cr
 #' \cr
 #'