Merge pull request #42 from jasenfinch/devel

v0.6.2
jasenfinch · Mar 29, 2023 · b07aacf · b07aacf
2 parents f33536b + 2ca5b09
commit b07aacf
Show file tree

Hide file tree

Showing 4 changed files with 14 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: metaboMisc
 Title: Miscellaneous Functions for Metabolomics Analyses
-Version: 0.6.1
+Version: 0.6.2
 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.
 URL: https://jasenfinch.github.io/metaboMisc/

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# metaboMisc 0.6.2
+
+* Fixed miss injection and batch correction detection for GC-MS data sets processed using xcms.
+
+* Fixed the feature summary for GC-MS data sets processed using xcms.
+
 # metaboMisc 0.6.1
 
 * Fix the missing `name` column in tables returned from `convertSampleInfo()`.

diff --git a/R/detect.R b/R/detect.R
@@ -59,7 +59,7 @@ setMethod('detectMissInjections',signature = 'MetaboProfile',
               mi <- x %>% 
                   processedData()
 
-              if (!is.list(mi)){
+              if (is.data.frame(mi)){
                   mi <- list(mi)   
               }
 
@@ -68,10 +68,10 @@ setMethod('detectMissInjections',signature = 'MetaboProfile',
 
               if (mi %>% 
                   names() %>% 
-                  is.na() %>% 
+                  {is.null(.) | is.na(.)} %>% 
                   any()) {
                   names(mi) <- replace(names(mi),
-                                       is.na(names(mi)),
+                                       is.null(names(mi)) | is.na(names(mi)),
                                        'NA')
               }
 
@@ -166,7 +166,7 @@ setMethod('detectBatchDiff',signature =  "MetaboProfile",
               TICdat <- x %>%
                   processedData()
 
-              if (!is.list(TICdat)){
+              if (is.data.frame(TICdat)){
                   TICdat <- list(TICdat)
               }
 
@@ -175,10 +175,10 @@ setMethod('detectBatchDiff',signature =  "MetaboProfile",
 
               if (TICdat %>% 
                   names() %>% 
-                  is.na() %>% 
+                  {is.null(.) | is.na(.)} %>% 
                   any()) {
                   names(TICdat) <- replace(names(TICdat),
-                                           is.na(names(TICdat)),
+                                           is.null(names(TICdat)) | is.na(names(TICdat)),
                                            'NA')
               }
 

diff --git a/R/summary.R b/R/summary.R
@@ -42,7 +42,7 @@ setMethod('featureSummary',signature = 'MetaboProfile',
 
 featSummary <- function(x){
 
-    if (!is.list(x)){
+    if (is.data.frame(x)){
         x <- list(x)
     }