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creating outdirs if doesn't exista and reading master file from backup

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This commit is contained in:
Tanushree Tunstall 2020-10-26 12:01:18 +00:00
parent c553ef3be0
commit 745f45eb6d
1 changed files with 15 additions and 6 deletions
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21
read_data.R
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@ -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)
########################################################################