new version for mQTL deprecation

.Rbuildignore

@@ -15,3 +15,5 @@
 ^docimages/speaq-github-workflow.png$
 ^revdep/.+$
 ^.gitattributes
+^\.github$
+^revdep$

.gitignore

@@ -7,3 +7,5 @@ doc
 .DS_Store
 
 revdep/.cache.rds
+/doc/
+/Meta/

.travis.yml

@@ -18,7 +18,6 @@ addons:
     packages:
     - r-cran-devtools
     - r-bioc-massspecwavelet
-    - r-cran-mqtl
     - r-cran-dosnow
     - r-cran-cluster
     - r-cran-data.table

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: speaq
-Version: 2.6.1
-Date: 2019-12-10
+Version: 2.7.0
+Date: 2022-05-20
 Title: Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations
 Author: Charlie Beirnaert, Trung Nghia Vu, Pieter Meysman, Kris Laukens and Dirk Valkenborg
 Maintainer: Charlie Beirnaert <charlie_beirnaert@icloud.com>
@@ -10,7 +10,6 @@ Depends:
 Imports:
     MassSpecWavelet,
     cluster,
-    mQTL,
     parallel,
     doSNOW,
     data.table,
@@ -36,4 +35,5 @@ Suggests:
 LazyData: true
 VignetteBuilder: knitr
 License: Apache License 2.0
-RoxygenNote: 7.0.2
+RoxygenNote: 7.2.0
+Encoding: UTF-8

NAMESPACE

@@ -47,7 +47,6 @@ importFrom(graphics,plot)
 importFrom(graphics,points)
 importFrom(gridExtra,grid.arrange)
 importFrom(impute,impute.knn)
-importFrom(mQTL,normalise)
 importFrom(missForest,missForest)
 importFrom(parallel,makeCluster)
 importFrom(parallel,stopCluster)

NEWS.md

@@ -1,3 +1,9 @@
+# speaq 2.6.2
+### 17/05/2022
+
+* Removing mQTL dependencies due to ending CRAN availability of mQTL package. Probabilistic quotient normalisation will not be available anymore in SCANT function. Also ended support of deprecated 'what' option in SCANT function in favor of the 'feature_orientation' designation. 
+
+
 # speaq 2.6.1
 ### 10/12/2019
 

R/SCANT.R

@@ -3,9 +3,8 @@
 #' This function allows the column-wise or row-wise scaling, normalization and transformation operations on a data matrix.
 #'
 #' @param data.matrix the data matrix to be scaled, normalized or transformed.
-#' @param type the operations to be performed, this can be multiple and are performed sequentially. Any of 'unit', 'pareto', 'log10', 'log2', 'center', 'range', 'vast', 'prob.Q' or 'max' are accepted.
+#' @param type the operations to be performed, this can be multiple and are performed sequentially. Any of 'unit', 'pareto', 'log10', 'log2', 'center', 'range', 'vast', or 'max' are accepted.
 #' @param feature_orientation default = "columns". This corresponds to the default feature matrix with samples as rows and features as columns. The other option is "rows": samples as columns and different features as different rows.
-#' @param what (deprecated, use feature_orientation) to specify on which to perform the operations (row or column).
 #'
 #' @return The scaled, normalized and/or transformed matrix.
 #'
@@ -23,22 +22,16 @@
 #' 
 #' @export
 #' 
-#' @importFrom mQTL normalise
 #' @importFrom stats sd
 #' 
-SCANT <- function(data.matrix, type = "unit", feature_orientation = "columns", what = NA) {
+SCANT <- function(data.matrix, type = "unit", feature_orientation = "columns") {
 
     for (N in seq_along(type)) {
         if (!(type[N] %in% c("unit", "pareto", "log10", "log2", "center", "range", "vast", "prob.Q", "max", "TotSum"))) {
             stop("No appropriate type of normalization/scaling selected")
         }
     }
 
-    if(!is.na(what)){
-        warning("The use of the 'what' parameter is deprecated. Please use 'feature_orientation' instead. For now feature_orientation has been set in accordance with the supplied 'what' parameter.")
-        feature_orientation = what
-    }
-
     if (!(feature_orientation %in% c("columns", "rows"))) {
         stop("No appropriate 'feature_orientation' is selected")
     }
@@ -88,11 +81,6 @@ SCANT <- function(data.matrix, type = "unit", feature_orientation = "columns", w
         if (Curr.type == "vast") {
             scaled.data <- apply(scaled.data, 2, function(x) ((x - mean(x)) * mean(x))/(stats::sd(x)^2))
         }
-        ## Quotient probabilistic normalisation
-        if (Curr.type == "prob.Q") {
-            scaled.data <- mQTL::normalise(scaled.data, "prob")
-            scaled.data <- scaled.data[[1]]
-        }
         if (Curr.type == "max") {
             scaled.data <- apply(scaled.data, 2, function(x) (x/max(x)))
         }

R/Winedata.R

@@ -11,7 +11,7 @@
 #' @keywords datasets
 #'
 #' @references  Larsen et al. (2006) An exploratory chemometric study of 1H-NMR spectra of table wines. J.Chemom. 20 (2006) 198-208
-#' (\href{http://onlinelibrary.wiley.com/doi/10.1002/cem.991/full}{Wiley Online Library})
+#' (\href{https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/abs/10.1002/cem.991}{Wiley Online Library})
 #'
 #' @source University of Copenhagen, Dept. of Food Science, Quality & Technology. Available at 'models.life.ku.dk/datasets'
 #'

cran-comments.Rmd

@@ -8,26 +8,22 @@ output: md_document
 MassSpecWavelet and impute are Bioconductor packages.
 
 ## Test environments
-* local OS X install, R 3.6.1
-* devtools win-builder, R oldrel 3.5.3 (2019-03-11)
-* devtools win-builder, R release 3.6.1 (2019-07-05)
-* devtools win-builder, R devel (unstable) (2019-12-02 r77499)
-* travis.ci Linux, x64, R release 3.6.1 (2017-01-27)
-* travis.ci Linux, x64, R devel (unstable) (2019-12-10 r77548) 
+* local OS X install, R 4.2.0
+* devtools win-builder, R release 4.2.0 (2022-04-22 ucrt)
+* devtools win-builder, R devel (2022-05-19 r82383 ucrt)
 
 
 ## R CMD check results
 There were no ERRORs or WARNINGs.
 
-Local OS X build generated 1 NOTE
+Local OS X build generated 0 NOTEs
 
-Travis.ci generated no NOTEs
+R-hub generatet 1 NOTE
 
 Win-builder generated 1 NOTE
 
 * Uses the superseded package: 'doSNOW': this is to provide continuously updated progress bars when performing parallel computations (not available in doParallel so far as doParallel calls the combine function only when all results have been accumulated). When this option is avalaible in doParallel the switch to this package will be made.
 
-* possibly mis-spelled words in DESCRIPTION: These words are not mis-spelled.
 
 
 ## Downstream dependencies