transform example

vignettes/03-rnaseq_analysis.Rmd

@@ -60,7 +60,7 @@ head(metaData)
 
 ## Prepare data for fitting
 
-The `prepareData2fit()` function serves the purpose of converting the counts matrix and sample metadata into a dataframe that is compatible with downstream **HTRfit** functions designed for model fitting. This function also includes an option to perform median ratio normalization on the data counts.
+The `prepareData2fit()` function serves the purpose of converting the counts matrix and sample metadata into a dataframe that is compatible with downstream **HTRfit** functions designed for model fitting. This function also includes an option to perform median ratio normalization and transformation on the data counts.
 
 
 ```{r example-prepareData, warning = FALSE, message = FALSE}
@@ -78,6 +78,14 @@ data2fit = prepareData2fit(
              metadata =  metaData, 
              normalization = T, 
              response_name = "kij")
+
+## -- apply + 1 transformation on each counts
+data2fit = prepareData2fit(
+             countMatrix = count_matrix, 
+             metadata =  metaData, 
+             normalization = T, 
+             transform = "x+1",
+             response_name = "kij")
 ```
 
 ## Fit model from your data