Fixed typos and added genotype path

scripts/1_definitions_and_setup.Rmd

@@ -43,6 +43,10 @@ This script asks the user to define or choose:
   + person id  
   + sex  
 * additional batch variables (up to 3)  
+* optionally:
+  + path for R packages
+  + path to the genotype data location
+  + prefix (project name) of the genotype files
 
 <br>  
 **Notes/Definitions:**  
@@ -52,9 +56,9 @@ The path name should not include the name of the github repository
 **Path to phenotype data:** The path to the data table containing phenotype information  
 The path name should include the name of data table itself. This file must be **.csv**  
 **Path to idat files:** The path to the raw files obtained from array  
-**Path to R package directories (optional):** The path to the personal directory for installing and loading packages. 
+**Path to R package directories (optional):** The path to a directory for installing and loading R packages. 
 This is needed if installation of R packages to the default R library are not permitted due to the lack of admin rights. 
-Thsi will enable R to install and load any needed packages without problems. 
+This will enable R to install and load any needed packages without problems. 
 Please make sure you have the needed writing permissions in this specified directory  
 **Array type:** "v1" or "v2". This stands for the different versions of the EPIC array  
 **Population ethnicity:** Choose "AFR", "AMR", "ASN", "EUR" or "Global". Global 
@@ -78,6 +82,9 @@ be listed as F, M, or W. If your sex data is described in a different way
 be considered in a batch check in script 8: plate, slide, array, row and column. Please 
 provide additional possible batch variables if needed as a character vector (up to 3, 
 add more if necessary). If not, please leave this field as is.  
++**Path to genotype files:** The path to the QC-ed genotype data in plink file format (.bed, .bim, .fam)  
++**Genotype project name:** Prefix of the genotype files, denoting the project (e.g. my_study_2020)  
+
 <br>  
 
 ## Directory structure
@@ -143,10 +150,11 @@ user_choices <- data.frame(
   "name_well_column" = name_well_column,
   "name_personid_column" = name_personid_column,
   "name_sex_column" = name_sex_column, 
-  "name_treatment_column" = name_treatment_column,
   "additional_batch_variable_1" = additional_batch_variable_1,
   "additional_batch_variable_2" = additional_batch_variable_2,
-  "additional_batch_variable_3" = additional_batch_variable_3
+  "additional_batch_variable_3" = additional_batch_variable_3,
+  "genotype_path" = genotype_path,
+  "genotype_projectname" = genotype_projectname
 )
 saveRDS(user_choices, "../data/user_choices.rds")