Merge pull request #43 from jasenfinch/devel

v0.7.8
aberHRML · Apr 20, 2021 · 5b2df43 · 5b2df43
2 parents d5c5b46 + 9755538
commit 5b2df43
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Showing 3 changed files with 11 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MFassign
 Title: Molecular Formula Assignment for High Resolution metabolomics
-Version: 0.7.7
+Version: 0.7.8
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: Molecular formula assignment for high resolution metabolomics.
 Depends: R (>= 3.5.0),

diff --git a/NAMESPACE b/NAMESPACE
@@ -83,9 +83,9 @@ importFrom(magrittr,set_names)
 importFrom(magrittr,set_rownames)
 importFrom(metabolyseR,analysisData)
 importFrom(metabolyseR,analysisParameters)
-importFrom(metabolyseR,correlationResults)
+importFrom(metabolyseR,analysisResults)
 importFrom(metabolyseR,dat)
-importFrom(metabolyseR,keepVariables)
+importFrom(metabolyseR,keepFeatures)
 importFrom(metabolyseR,metabolyse)
 importFrom(metabolyseR,sinfo)
 importFrom(methods,new)

diff --git a/R/calcCorrelations-method.R b/R/calcCorrelations-method.R
@@ -1,4 +1,4 @@
-#' @importFrom metabolyseR analysisParameters metabolyse correlationResults keepVariables analysisData dat sinfo
+#' @importFrom metabolyseR analysisParameters metabolyse analysisResults keepFeatures analysisData dat sinfo
 #' @importFrom magrittr set_rownames
 #' @importFrom stats cutree dist hclust
 
@@ -38,16 +38,19 @@ setMethod('calcCorrelations',signature = 'Assignment',function(assignment){
       split(.$Group) %>%
       parLapply(cl = clus,function(f){
         analysisData(assignment@data,tibble(ID = 1:nrow(assignment@data))) %>%
-          keepVariables(variables = f$Feature) %>%
+          keepFeatures(features = f$Feature) %>%
           {metabolyse(dat(.),sinfo(.),p,verbose = FALSE)} %>% 
-          correlationResults()
+          analysisResults(element = 'correlations')
       }) %>%
       bind_rows(.id = 'RT Group')
     stopCluster(clus)
 
   } else {
-    cors <- metabolyse(assignment@data,tibble(ID = 1:nrow(assignment@data)),p,verbose = F) %>%
-      correlationResults()  
+    cors <- metabolyse(assignment@data,
+                       tibble(ID = 1:nrow(assignment@data)),
+                       p,
+                       verbose = FALSE) %>%
+      analysisResults(element = 'correlations') 
   }
 
   assignment@correlations <- cors