diff --git a/read_data.R b/read_data.R
index df50cec..23ae796 100644
--- a/read_data.R
+++ b/read_data.R
@@ -9,9 +9,13 @@ getwd()
 source("Header_TT.R")
 ########################################################################
 # TODO: turn this to a repo
-all_df <- read.csv("/home/pub/Work/MOSAIC/MOSAIC_from_work/MASTER/MOSAIC_2015_MASTER_Aki_stata_20150721/Mosaic_master_file_from_stata.csv"
+all_df <- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mosaic_master_file_from_stata.csv"
                    , fileEncoding='latin1') 
-#hc_data<- 
+
+hc_data<- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mediators_for_HC.csv")
+str(hc_data)
+table(hc_data$Timepoint, hc_data$Sample)
+
 # meta data columns                   
 meta_data_cols = c("mosaic", "gender", "age", "adult", "flustat", "type"
                    , "obesity", "obese2", "height", "height_unit", "weight"
@@ -23,7 +27,12 @@ all(meta_data_cols%in%colnames(all_df))
 
 metadata_all = all_df[, meta_data_cols]
 ########################################################################
-#
-#outdir = 
-#outdir_plots = 
-outdir_stats = paste0("~/git/mosaic_2020/output/stats/")
+outdir = "~/git/mosaic_2020/output/"
+ifelse(!dir.exists(outdir), dir.create(outdir), FALSE)
+
+outdir_stats = "~/git/mosaic_2020/output/stats/"
+ifelse(!dir.exists(outdir_stats), dir.create(outdir_stats), FALSE)
+
+outdir_plots = "~/git/mosaic_2020/output/plots/"
+ifelse(!dir.exists(outdir_plots), dir.create(outdir_plots), FALSE)
+########################################################################