Merge pull request #193 from WackerO/deseq_text

Add DESeq text to report

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [[#193](https://github.com/nf-core/differentialabundance/pull/193)] - Add DESeq2 text to report ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#192](https://github.com/nf-core/differentialabundance/pull/192)] - Add scree plot in report ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#188](https://github.com/nf-core/differentialabundance/pull/188)] - Add option to cluster all features ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 

assets/differentialabundance_report.Rmd

@@ -697,11 +697,17 @@ foo <- lapply(informative_variables[iv_min_group_sizes > 2], function(iv){
     }
   }
 })
-
 ```
 
 ## Differential analysis
 
+```{r, echo=FALSE, results='asis', eval=params$study_type %in% c('rnaseq')}
+# For DESeq2, add some more explanation to the report
+cat(paste0(
+"The `DESeq2 R` package was used for differential analysis. p-values were adjusted with the ", params$deseq2_p_adjust_method, " method to reduce the number of false positives. ", ucfirst(params$features_type), "s were considered differential if, for the respective contrast, the adjusted p-value was equal to or lower than ", params$deseq2_alpha, " and the absolute log2 fold change was equal to or higher than ", params$deseq2_lfc_threshold, "."
+))
+```
+
 ### Differential `r params$features_type` `r params$study_abundance_type` {.tabset}
 
 ```{r, echo=FALSE, results='asis'}
@@ -879,6 +885,7 @@ make_params_table('exploratory analysis', 'exploratory_', remove_pattern = TRUE)
 
 ## Differential analysis
 
+
 ```{r, echo=FALSE, results='asis'}
 if (params$study_type == 'rnaseq'){
   make_params_table('DESeq2', 'deseq2_', remove_pattern = TRUE)