Merge pull request #49 from aberHRML/devel

v2.5.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: binneR
 Title: Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
-Version: 2.4.2
+Version: 2.5.0
 Authors@R: person("Jasen", "Finch", email = "[email protected]", role = c("aut", "cre"))
 Description: A spectral binning approach for high resolution flow infusion mass spectrometry data.
 biocViews: MassSpectrometry, Metabolomics
@@ -34,9 +34,6 @@ Collate:
     binParameters.R
     spectralBinning-method.R
     show-method.R
-    info-method.R
-    binnedData-method.R
-    accurateData-method.R
     get.R
     calc.R
     readFiles.R
@@ -47,6 +44,7 @@ Collate:
     singleSample.R
     readBinningParameters.R
     reexports.R
+    access.R
 Suggests: 
     knitr,
     rmarkdown,

NAMESPACE

@@ -16,16 +16,20 @@ exportMethods("cls<-")
 exportMethods("scans<-")
 exportMethods(accurateData)
 exportMethods(binnedData)
+exportMethods(binningParameters)
 exportMethods(cls)
-exportMethods(info)
+exportMethods(creationDate)
+exportMethods(filePaths)
 exportMethods(plotBin)
 exportMethods(plotCentrality)
 exportMethods(plotChromatogram)
 exportMethods(plotFingerprint)
 exportMethods(plotPurity)
 exportMethods(plotTIC)
+exportMethods(sampleInfo)
 exportMethods(scans)
 exportMethods(show)
+exportMethods(version)
 importFrom(cli,console_width)
 importFrom(crayon,blue)
 importFrom(crayon,green)

NEWS.md

@@ -1,3 +1,17 @@
+# binneR v2.5.0
+
+* S4 class [`Binalysis`](https://aberhrml.github.io/binneR/reference/Binalysis-class.html) now inherits from S4 class [`BinParameters`](https://aberhrml.github.io/binneR/reference/BinParameters-class.html).
+
+* Fixed retrieval of example data in the usage [vignette](https://aberhrml.github.io/binneR/articles/binneR.html)
+
+* `version` and `creation_date` slots added to [`Binalysis`](https://aberhrml.github.io/binneR/reference/Binalysis-class.html) S4 class.
+
+* Added additional accessor [methods](file:///home/jasen/Documents/tools/R-package-dev/binneR/docs/reference/results.html) for the [`Binalysis`](https://aberhrml.github.io/binneR/reference/Binalysis-class.html) S4 class.
+
+* Fixed declaration of generics to ensure they are declared as standard generics.
+
+* Added validators for [`Binalysis`](https://aberhrml.github.io/binneR/reference/Binalysis-class.html) S4 class to ensure that sample information contains the correct fields and that the file names in the specified paths match those in the sample information.
+
 # binneR v2.4.2
 
 * Bin measures are now correctly averaged across samples in [`binneR::plotCentrality()`](https://aberHRML.github.io/binneR/reference/plotCentrality.html) and [`binneR::plotPurity()`](https://aberHRML.github.io/binneR/reference/plotPurity.html).

R/access.R

@@ -0,0 +1,92 @@
+#' Binalysis class get methods
+#' @rdname results
+#' @description Methods for accessing spectral binning results from the  Binalysis S4 class.
+#' @param x S4 object of class Binalysis
+#' @details 
+#' \itemize{
+#'  \item{version}{ - Extract package version used to create the object.}
+#'  \item{creationDate}{ - Extract the creation date of the object.}
+#'  \item{filePaths}{ - Extract the sample file paths.}
+#'  \item{sampleInfo}{ - Extract sample meta information.}
+#'  \item{binnedData}{ - Extract a binned data intensity matrix.}
+#'  \item{accurateData}{ - Extract sample-wise accurate mass data and bin measures.}
+#'  \item{binningParametesr}{Extract the binning parameters.}
+#' }
+#' @seealso \code{\link{Binalysis-class}}, \code{\link{binneRlyse}}
+#' @export
+
+setMethod('version',signature = 'Binalysis',
+					function(x){
+						x@version
+					})
+
+#' @rdname results
+#' @export
+
+setMethod('creationDate',signature = 'Binalysis',
+					function(x){
+						x@creation_date
+					})
+
+#' @rdname results
+#' @export
+
+setMethod('filePaths',signature = 'Binalysis',
+					function(x){
+						x@file_paths
+					})
+
+#' @rdname results
+#' @export
+
+setMethod('sampleInfo',signature = 'Binalysis',
+					function(x){
+						x@sample_info
+					})
+
+#' @rdname results
+#' @export
+
+setMethod('binnedData',signature = 'Binalysis',
+					function(x){
+						x@binned_data
+					})
+
+setMethod('binnedData<-',signature = 'Binalysis',
+					function(x,value){
+						x@binned_data <- value
+						return(x)
+					})
+
+#' @rdname results
+#' @export
+
+setMethod('accurateData',signature = 'Binalysis',
+					function(x){
+						x@accurate_mz
+					})
+
+setMethod('accurateData<-',signature = 'Binalysis',
+					function(x,value){
+						x@accurate_mz <- value
+						return(x)
+					})
+
+#' @rdname results
+#' @export
+
+setMethod('binningParameters',signature = 'Binalysis',
+					function(x){
+						as(x,'BinParameters')
+					})
+
+setMethod('spectra',signature = 'Binalysis',
+					function(x){
+						x@spectra
+					})
+
+setMethod('spectra<-',signature = 'Binalysis',
+					function(x,value){
+						x@spectra <- value
+						return(x)
+					})

R/allClasses.R

@@ -17,27 +17,80 @@ setClass('BinParameters',
 #' Spectral binning analysis class
 #' @description An S4 class to store spectrally binned data and accurate 
 #' mass information.
-#' @slot binLog date and time of initiation of spectral binning
-#' @slot binParameters object of class BinParameters containing the 
-#' parameters for spectral binning 
-#' @slot files file paths for raw data
-#' @slot info tibble containing runinfo data
-#' @slot binnedData list containing tibbles of spectrally binned data 
+#' @slot version package version
+#' @slot creation_date creation date
+#' @slot file_paths file paths for raw data
+#' @slot sample_info tibble containing runinfo data
+#' @slot binned_data list containing tibbles of spectrally binned data 
 #' for each acquisition mode
-#' @slot accurateMZ tibble containin accurate mass information
+#' @slot accurate_mz tibble containin accurate mass information
 #' @slot spectra list containing tibbles of headers and class master 
 #' mix fingerprints
 #' @seealso \code{\link{binneRlyse}} 
 #' @export
 
 setClass('Binalysis',
          slots = list(
-             binLog = 'character',
-             binParameters = 'BinParameters',
-             files = 'character',
-             info = 'tbl_df',
-             binnedData = 'list',
-             accurateMZ = 'tbl_df',
+             version = 'character',
+             creation_date = 'character',
+             file_paths = 'character',
+             sample_info = 'tbl_df',
+             binned_data = 'list',
+             accurate_mz = 'tbl_df',
              spectra = 'list'
-         )
+         ),
+				 contains = 'BinParameters',
+				 prototype = list(
+				 	version = packageVersion('binneR') %>%
+				 		as.character(),
+				 	creation_date = date(),
+				 	sample_info = tibble(
+				 		fileOrder = character(),
+				 		injOrder = numeric(),
+				 		fileName = character(),
+				 		batch = numeric(),
+				 		block = numeric(),
+				 		name = character(),
+				 		class = character()
+				 	),
+				 	accurate_mz = tibble()
+				 )
 )
+
+setValidity('Binalysis',function(object){
+	necessary_names <- c('fileOrder','injOrder','fileName','batch','block','name','class')
+
+	info_names <- object %>%
+		sampleInfo() %>%
+		colnames()
+
+	presence <- necessary_names %in% info_names
+
+	if (FALSE %in% presence) {
+		str_c('Sample information should contain the following column names: ',
+					str_c(necessary_names,collapse = ', '),
+					'.')
+	} else {
+		TRUE
+	}
+})
+
+setValidity('Binalysis',function(object){
+	file_path_names <- object %>%
+		filePaths() %>%
+		basename()
+
+	info_file_names <- object %>%
+		sampleInfo() %>%
+		.$fileName
+
+	matching <- file_path_names == info_file_names
+
+	if (FALSE %in% matching) {
+		'File names in paths do not match file names in the sample information.'
+	} else {
+		TRUE
+	}
+
+
+})