diff --git a/vignettes/RAIDS.Rmd b/vignettes/RAIDS.Rmd
index cffa57fd..913f3b09 100644
--- a/vignettes/RAIDS.Rmd
+++ b/vignettes/RAIDS.Rmd
@@ -133,7 +133,7 @@ These steps are described in detail in the following.
### 1.1 Create a directory structure
-First, a specific directory structure must be created. The structure must
+First, a specific directory structure should be created. The structure must
correspond to this:
```
@@ -151,8 +151,7 @@ workingDirectory/
This following running example creates a temporary working directory structure
-when the demo samples will be run. Some sub-directories in
-*workingDirectory/data* will be created in subsequent steps.
+when the example will be run.
```{r createDir, echo=TRUE, eval=TRUE, collapse=TRUE, warning=FALSE, message=FALSE}
@@ -167,6 +166,7 @@ if (!dir.exists(pathWorkingDirectory)) {
dir.create(pathWorkingDirectory)
dir.create(pathWorkingDirectoryData)
dir.create(file.path(pathWorkingDirectoryData, "refGDS"))
+ dir.create(file.path(pathWorkingDirectoryData, "profileGDS"))
}
```
@@ -252,8 +252,8 @@ refGenotype <- file.path(pathReference, "ex1_good_small_1KG.gds")
refAnnotation <- file.path(pathReference, "ex1_good_small_1KG_Annot.gds")
#############################################################################
-## The output directories inside workingDirectory/data must be created
-## (pathProfileGDS will be used as input later)
+## The output profileGDS directory, inside workingDirectory/data, must be
+## created (pathProfileGDS will be used as input later)
#############################################################################
pathProfileGDS <- file.path(pathWorkingDirectoryData, "profileGDS")
@@ -271,7 +271,8 @@ if (!dir.exists(pathProfileGDS)) {
With the 1KG reference, we recommend sampling 30 donor profiles per population.
For reproducibility, be sure to use the same random-number generator seed.
-In the following code, only 2 profiles per population are sampled:
+In the following code, only 2 profiles per population are sampled from the
+demo population GDS file:
```{r sampling, echo=TRUE, eval=TRUE, collapse=TRUE, warning=FALSE, message=FALSE}
@@ -429,7 +430,7 @@ createAUROCGraph(dfAUROC=resOut$paraSample$dfAUROC, title="Example ex1")
```
-In this specific demonstration, the performances are lower than expected
+In this specific example, the performances are lower than expected
with a real profile and a complete reference population file.