Merge pull request #82 from jasenfinch/devel

v0.14.5
jasenfinch · Nov 11, 2021 · 051fc5d · 051fc5d
2 parents 43a68c9 + ec421b7
commit 051fc5d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: metabolyseR
 Title: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data
-Version: 0.14.4
+Version: 0.14.5
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data.
 URL: https://jasenfinch.github.io/metabolyseR

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# metabolyseR 0.14.5
+
+* Correlation analysis results now include an absolute correlation coefficient column by which the results are also arranged in descending order.
+
 # metabolyseR 0.14.4
 
 * Console output from [`imputeAll()`](https://jasenfinch.github.io/metabolyseR/reference/impute.html) now suppressed.

diff --git a/R/correlations.R b/R/correlations.R
@@ -156,9 +156,11 @@ doCorrelations <- function(d,
     rename(Intensity1 = Intensity) %>%
     left_join(intensity, by = c('Feature2' = 'Feature')) %>%
     rename(Intensity2 = Intensity) %>%
-    mutate(log2IntensityRatio = log2(Intensity1/Intensity2)) %>%
-    select(Feature1,Feature2,log2IntensityRatio,r,p,n)  %>% 
-    na.omit()
+    mutate(`|r|` = abs(r),
+           log2IntensityRatio = log2(Intensity1/Intensity2)) %>%
+    select(Feature1,Feature2,log2IntensityRatio,r,`|r|`,p,n)  %>% 
+    na.omit() %>% 
+    arrange(desc(`|r|`))
 
   return(rs)
 }
diff --git a/R/metabolyseR.R b/R/metabolyseR.R
@@ -7,5 +7,5 @@ globalVariables(
     'Occupancy','adjustedPvalue','adjusted.p.value','Label','response',
     '-log10(p)','DF1','Sample1','Proximity','Dimension 1','Dimension 2',
     'x','.level','sensitivity','specificity','Mode','RSD','Median','Colour',
-    'Index','TIC','y','label','batch','correction','N','term','Metric','Frequency'
+    'Index','TIC','y','label','batch','correction','N','term','Metric','Frequency','|r|'
   ))
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/metabolyseR.html b/docs/articles/metabolyseR.html
diff --git a/docs/articles/modelling.html b/docs/articles/modelling.html
diff --git a/docs/articles/modelling_files/figure-html/outlier-detect-1.png b/docs/articles/modelling_files/figure-html/outlier-detect-1.png
diff --git a/docs/articles/modelling_files/figure-html/regression-mds-1.png b/docs/articles/modelling_files/figure-html/regression-mds-1.png
diff --git a/docs/articles/pre_treatment.html b/docs/articles/pre_treatment.html
diff --git a/docs/articles/quick_start.html b/docs/articles/quick_start.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html