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minor tweaks to read_data.R

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Tanushree Tunstall 2020-10-26 12:11:08 +00:00
parent 745f45eb6d
commit 8e06f382c0
1 changed files with 20 additions and 13 deletions
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33
read_data.R
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@ -8,14 +8,23 @@ getwd()
# load libraries, packages and local imports
source("Header_TT.R")
########################################################################
# TODO: turn this to a repo
maindir = "~/git/mosaic_2020/"
outdir = paste0(maindir, "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)
########################################################################
# static file read: csv
#==============
# all patients
#==============
all_df <- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mosaic_master_file_from_stata.csv"
, fileEncoding='latin1')
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"
@ -26,13 +35,11 @@ meta_data_cols%in%colnames(all_df)
all(meta_data_cols%in%colnames(all_df))
metadata_all = all_df[, meta_data_cols]
########################################################################
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)
#============
# hc
#============
#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)
########################################################################