fix univariate mann

pcastellanoescuder · Mar 9, 2024 · 00656f1 · 00656f1
1 parent 51a4ac3
commit 00656f1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: POMA
 Title: Tools for Omics Data Analysis   
-Version: 1.13.23
+Version: 1.13.24
 Authors@R: 
     c(person(given = "Pol",
              family = "Castellano-Escuder",

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# POMA 1.13.23
+# POMA 1.13.24
 
 * New POMA theme and colorblind-friendly palette
 * Available sample normalization (sum and quantile)

diff --git a/R/PomaUnivariate.R b/R/PomaUnivariate.R
@@ -234,8 +234,22 @@ PomaUnivariate <- function(data,
     }
 
     suppressWarnings({
-      result <- data.frame(pvalue = apply(to_univariate, 2, function(x){wilcox.test(x ~ as.factor(group_factor),
-                                                                                    paired = paired)$p.value})) %>% 
+      mann_result <- data.frame(pvalue = apply(to_univariate, 2, function(x) {
+        if (!paired) {
+          res <- wilcox.test(x ~ as.factor(group_factor), 
+                             data = data.frame(x, as.factor(group_factor)), 
+                             paired = FALSE)
+        } else {
+          group1 <- x[group_factor == levels(group_factor)[1]]
+          group2 <- x[group_factor == levels(group_factor)[2]]
+
+          res <- wilcox.test(group1, group2, 
+                             paired = TRUE)
+        }
+        res$p.value
+      }))
+
+      result <- mann_result %>% 
         tibble::rownames_to_column("feature") %>%
         dplyr::mutate(adj_pvalue = p.adjust(pvalue, method = adjust)) %>%
         dplyr::bind_cols(group_means, group_sd) %>%

diff --git a/README.Rmd b/README.Rmd
@@ -16,7 +16,7 @@ output: github_document
 | _BioC_ branch 	| Status 	| Version 	| Dependencies 	| Rank 	|
 |-	|-	|-	|-	|-	|
 | [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) 	| [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) 	| [![BioC released version](https://img.shields.io/badge/release%20version-1.12.0-blue.svg)](https://www.bioconductor.org/packages/POMA) 	| [![Dependencies](http://bioconductor.org/shields/dependencies/release/POMA.svg)](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) 	| [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) 	|
-| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) 	| [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.23-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) 	| [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) 	|
+| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) 	| [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.24-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) 	| [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) 	|
 
   <!-- badges: end -->
 

diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/li
 | *BioC* branch                                                           | Status                                                                                                                                                  | Version                                                                                                                                             | Dependencies                                                                                                                                         | Rank                                                                                                                         |
 |-------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------|
 | [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) | [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) | [![BioC released version](https://img.shields.io/badge/release%20version-1.12.0-blue.svg)](https://www.bioconductor.org/packages/POMA)              | [![Dependencies](http://bioconductor.org/shields/dependencies/release/POMA.svg)](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |
-| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html)     | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/)       | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.23-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since)     | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA)   |
+| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html)     | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/)       | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.24-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since)     | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA)   |
 
 <!-- badges: end -->