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.