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renamed file to reflect data_extraction_mediator

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Tanushree Tunstall 2020-11-27 17:47:05 +00:00
parent 52a2453327
commit 3a380a5be1
11 changed files with 95 additions and 1963 deletions
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26
read_data.R
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@ -7,6 +7,8 @@ getwd()
########################################################################
# load libraries, packages and local imports
source("Header_TT.R")
source("colnames_clinical_meds.R")
########################################################################
maindir = "~/git/mosaic_2020/"
outdir = paste0(maindir, "output/")
@ -15,6 +17,12 @@ ifelse(!dir.exists(outdir), dir.create(outdir), FALSE)
outdir_stats = paste0(maindir, "output/stats/")
ifelse(!dir.exists(outdir_stats), dir.create(outdir_stats), FALSE)
outdir_stats_na = paste0(maindir, "output/stats/non_asthmatics/")
ifelse(!dir.exists(outdir_stats_na), dir.create(outdir_stats_na), FALSE)
outdir_stats_ns = paste0(maindir, "output/stats/non_severe/")
ifelse(!dir.exists(outdir_stats_ns), dir.create(outdir_stats_ns), FALSE)
outdir_plots = paste0(maindir, "output/plots/")
ifelse(!dir.exists(outdir_plots), dir.create(outdir_plots), FALSE)
########################################################################
@ -26,22 +34,22 @@ all_df <- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mosaic_master_
, fileEncoding = 'latin1')
# meta data columns
meta_data_cols = c("mosaic", "gender", "age"
, "adult"
, "flustat", "type"
, "obesity"
#meta_data_cols = c("mosaic", "gender", "age"
# , "adult"
# , "flustat", "type"
# , "obesity"
#, "obese2"
#, "height", "height_unit"
#, "weight", "weight_unit"
#, "ia_height_ftin", "ia_height_m", "ia_weight"
#, "visual_est_bmi", "bmi_rating"
)
# )
# check if these columns to select are present in the data
meta_data_cols%in%colnames(all_df)
all(meta_data_cols%in%colnames(all_df))
metadata_all = all_df[, meta_data_cols]
meta_clinical_cols%in%colnames(all_df)
if ( all(meta_clinical_cols%in%colnames(all_df)) ){
metadata_all = all_df[, meta_clinical_cols]
}
#==============
# adult patients