diff --git a/CHANGELOG.md b/CHANGELOG.md index cdfb738a..89ad43e1 100644 --- a/CHANGELOG.md +++ b/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)) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index 7d3d2a56..e5d992f5 100644 --- a/assets/differentialabundance_report.Rmd +++ b/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)