70 lines
No EOL
2.2 KiB
R
Executable file
70 lines
No EOL
2.2 KiB
R
Executable file
#!/usr/bin/Rscript
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getwd()
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setwd("~/git/mosaic_2020/")
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getwd()
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########################################################################
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# TASK: read data
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########################################################################
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# load libraries, packages and local imports
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source("Header_TT.R")
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########################################################################
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maindir = "~/git/mosaic_2020/"
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outdir = paste0(maindir, "output/")
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ifelse(!dir.exists(outdir), dir.create(outdir), FALSE)
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outdir_stats = paste0(maindir, "output/stats/")
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ifelse(!dir.exists(outdir_stats), dir.create(outdir_stats), FALSE)
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outdir_plots = paste0(maindir, "output/plots/")
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ifelse(!dir.exists(outdir_plots), dir.create(outdir_plots), FALSE)
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########################################################################
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# static file read: csv
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#==============
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# all patients
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#==============
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all_df <- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mosaic_master_file_from_stata.csv"
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, fileEncoding = 'latin1')
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# meta data columns
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meta_data_cols = c("mosaic", "gender", "age"
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, "adult"
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, "flustat", "type"
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, "obesity"
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, "obese2"
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, "height", "height_unit"
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, "weight", "weight_unit"
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, "ia_height_ftin", "ia_height_m", "ia_weight"
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, "visual_est_bmi", "bmi_rating"
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)
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# check if these columns to select are present in the data
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meta_data_cols%in%colnames(all_df)
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all(meta_data_cols%in%colnames(all_df))
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metadata_all = all_df[, meta_data_cols]
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#==============
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# adult patients
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#==============
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adult_df = all_df[all_df$age>=18,]
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if (table(adult_df$adult == 1)[[1]] == nrow(adult_df) ){
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cat ("PASS: adult df extracted successfully")
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} else{
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cat ("FAIL: adult df number mismatch!")
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}
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#==============
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# FLU positive: adult patients
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#==============
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# extract the flu positive population
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fp_adults = adult_df[adult_df$flustat == 1,]
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#============
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# hc
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#============
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#hc_data<- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mediators_for_HC.csv")
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#str(hc_data)
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#table(hc_data$Timepoint, hc_data$Sample)
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######################################################################## |