Reformat source files using styler.

R/access.R

@@ -2,7 +2,7 @@
 #' @rdname results
 #' @description Methods for accessing spectral binning results from the  Binalysis S4 class.
 #' @param x S4 object of class Binalysis
-#' @details 
+#' @details
 #' \itemize{
 #'  \item{version}{ - Extract package version used to create the object.}
 #'  \item{creationDate}{ - Extract the creation date of the object.}
@@ -15,78 +15,100 @@
 #' @seealso \code{\link{Binalysis-class}}, \code{\link{binneRlyse}}
 #' @export
 
-setMethod('version',signature = 'Binalysis',
-					function(x){
-						x@version
-					})
+setMethod("version",
+  signature = "Binalysis",
+  function(x) {
+    x@version
+  }
+)
 
 #' @rdname results
 #' @export
 
-setMethod('creationDate',signature = 'Binalysis',
-					function(x){
-						x@creation_date
-					})
+setMethod("creationDate",
+  signature = "Binalysis",
+  function(x) {
+    x@creation_date
+  }
+)
 
 #' @rdname results
 #' @export
 
-setMethod('filePaths',signature = 'Binalysis',
-					function(x){
-						x@file_paths
-					})
+setMethod("filePaths",
+  signature = "Binalysis",
+  function(x) {
+    x@file_paths
+  }
+)
 
 #' @rdname results
 #' @export
 
-setMethod('sampleInfo',signature = 'Binalysis',
-					function(x){
-						x@sample_info
-					})
+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)
-					})
+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)
-					})
+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)
-					})
+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

@@ -1,96 +1,96 @@
 #' Spectral binning parameters class
 #' @description An S4 class to store spectral binning parameters.
 #' @slot scans numeric vector containing the scan indexes to use for binning
-#' @slot cls the column of class labels to use for aggregating accurate 
-#' mass data. Defaults to NULL where accurate mass data will be averaged 
+#' @slot cls the column of class labels to use for aggregating accurate
+#' mass data. Defaults to NULL where accurate mass data will be averaged
 #' across all samples
 #' @seealso \code{\link{binParameters}}
 #' @export
 
-setClass('BinParameters',
-         slots = list(
-             scans = 'numeric',
-             cls = 'character'
-         ),
+setClass("BinParameters",
+  slots = list(
+    scans = "numeric",
+    cls = "character"
+  ),
 )
 
 #' Spectral binning analysis class
-#' @description An S4 class to store spectrally binned data and accurate 
+#' @description An S4 class to store spectrally binned data and accurate
 #' mass information.
 #' @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 
+#' @slot binned_data list containing tibbles of spectrally binned data
 #' for each acquisition mode
 #' @slot accurate_mz tibble containin accurate mass information
-#' @slot spectra list containing tibbles of headers and class master 
+#' @slot spectra list containing tibbles of headers and class master
 #' mix fingerprints
-#' @seealso \code{\link{binneRlyse}} 
+#' @seealso \code{\link{binneRlyse}}
 #' @export
 
-setClass('Binalysis',
-         slots = list(
-             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()
-				 )
+setClass("Binalysis",
+  slots = list(
+    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) {
+  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() %>%
-		.$fileName
-
-	matching <- file_path_names == info_file_names
-
-	if (FALSE %in% matching) {
-		'File names in paths do not match file names in the sample information.'
-	} else {
-		TRUE
-	}
-
-
+setValidity("Binalysis", function(object) {
+  file_path_names <- object %>%
+    filePaths() %>%
+    basename()
+
+  info_file_names <- object %>%
+    sampleInfo() %>%
+    .$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
+  }
 })