From d74101d71c8e5975c7e91f07d8fa8a5f5cb5c49e Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Mon, 25 Mar 2024 17:30:04 +0100 Subject: [PATCH] docs: make example `config/config.yaml` consistent with `config/samples.tsv` --- config/config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index 220ad38..f11b015 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -37,23 +37,23 @@ diffexp: variables_of_interest: treatment_1: # any fold change will be relative to this factor level - base_level: B + base_level: untreated treatment_2: # any fold change will be relative to this factor level - base_level: C + base_level: untreated # variables whose effect you want to model to separate them from your # variables_of_interest batch_effects: - jointly_handled # contrasts for the deseq2 results method to determine fold changes contrasts: - A-vs-B_treatment_1: + treatment_1: # must be one of the variables_of_interest, for details see: # https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#contrasts variable_of_interest: treatment_1 # must be a level present in the variable_of_interest that is not the # base_level specified above - level_of_interest: A + level_of_interest: treated # The default model includes all interactions among variables_of_interest # and batch_effects added on. For the example above this implicitly is: # model: ~jointly_handled + treatment_1 * treatment_2