Merge pull request #23 from jasenfinch/devel

v0.4.2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metaboMisc
 Title: Miscellaneous Functions for Metabolomics Analyses
-Version: 0.4.1
+Version: 0.4.2
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: Miscellaneous helper functions for metabolomics analyses that do not yet have a permanent home.
 biocViews: Metabolomics
@@ -39,6 +39,7 @@ Collate:
     plotRSD.R
     export.R
     parallel.R
+    featureSummary.R
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true

NAMESPACE

@@ -1,15 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
-export(addAssignments)
-export(detectBatchDiff)
-export(detectMissInjections)
-export(detectPairwises)
-export(export)
 export(filterCorrelations)
-export(reduce)
 export(suitableParallelPlan)
 export(theme_neat)
 exportMethods(export)
+exportMethods(featureSummary)
 exportMethods(plotRSD)
 exportMethods(preTreatModes)
 importClassesFrom(MFassign,Assignment)
@@ -33,6 +28,7 @@ importFrom(dplyr,group_by_all)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,n)
+importFrom(dplyr,n_distinct)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(future,availableCores)

NEWS.md

@@ -1,3 +1,7 @@
+# metaboMisc 0.4.2
+
+* Added `metaboMisc::featureSummary()` to summarise spectral features in the [`Binalysis`](https://aberhrml.github.io/binneR/reference/Binalysis-class.html) S4 class.
+
 # metaboMisc 0.4.1
 
 * Added a `NEWS.md` file to track changes to the package.

R/allGenerics.R

@@ -5,43 +5,43 @@ setGeneric("preTreatModes", function(processedData,parameters,verbose = T) {
 })
 
 #' @rdname detectBatchDiff
-#' @export
 
 setGeneric('detectBatchDiff',function(x, by = 'block', pthresh = 0.05){
     standardGeneric('detectBatchDiff')
 })
 
 #' @rdname detectMissInjections
-#' @export
 
 setGeneric('detectMissInjections',function(x,idx = 'fileOrder'){
     standardGeneric('detectMissInjections')
 })
 
 #' @rdname detectPairwises
-#' @export
 
 setGeneric('detectPairwises',function(x,cls,type){
     standardGeneric('detectPairwises')
 })
 
 #' @rdname addAssignments
-#' @export 
 
 setGeneric('addAssignments',function(analysis,assignment){
     standardGeneric('addAssignments')
 })
 
 #' @rdname reduce
-#' @export 
 
 setGeneric('reduce',function(x, isotopes = T, adducts = T, unknowns = F){
     standardGeneric('reduce')
 })
 
 #' @rdname export
-#' @export
 
 setGeneric('export',function(analysis,outPath = '.'){
     standardGeneric('export')
 })
+
+#' @rdname featureSummary
+
+setGeneric('featureSummary',function(x){
+    standardGeneric('featureSummary')
+})

R/featureSummary.R

@@ -0,0 +1,30 @@
+#' Summarise features
+#' @rdname featureSummary
+#' @description Summarise spectral binning features.
+#' @param x S4 object of class Binalysis
+#' @importFrom dplyr n_distinct
+#' @export
+
+setMethod('featureSummary',signature = 'Binalysis',
+          function(x){
+              x %>%
+                  binnedData() %>%
+                  map(~{{
+                      .x %>%
+                          rowid_to_column(var = 'Sample') %>%
+                          gather('Feature','Intensity',-Sample)
+                  }}) %>%
+                  bind_rows() %>%
+                  mutate(Mode = str_sub(Feature,1,1)) %>%
+                  group_by(Mode) %>%
+                  summarise(
+                      `Number of bins` = n_distinct(Feature),
+                      `Missing Data (%)` = round(length(which(Intensity == 0)) / 
+                                                     length(Intensity) * 100,2),
+                      .groups = 'drop') %>%
+                  {{
+                      .$Mode[.$Mode == 'n'] = 'Negative'
+                      .$Mode[.$Mode == 'p'] = 'Positive'
+                      .
+                  }}
+          })