38 lines
1.6 KiB
R
38 lines
1.6 KiB
R
#!/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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# TODO: turn this to a repo
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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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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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# meta data columns
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meta_data_cols = c("mosaic", "gender", "age", "adult", "flustat", "type"
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, "obesity", "obese2", "height", "height_unit", "weight"
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, "weight_unit", "visual_est_bmi", "bmi_rating")
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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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outdir = "~/git/mosaic_2020/output/"
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ifelse(!dir.exists(outdir), dir.create(outdir), FALSE)
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outdir_stats = "~/git/mosaic_2020/output/stats/"
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ifelse(!dir.exists(outdir_stats), dir.create(outdir_stats), FALSE)
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outdir_plots = "~/git/mosaic_2020/output/plots/"
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ifelse(!dir.exists(outdir_plots), dir.create(outdir_plots), FALSE)
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########################################################################
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