separated checks from flu stats and added bonferrroni p
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8e06f382c0
commit
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2 changed files with 62 additions and 47 deletions
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@ -12,10 +12,10 @@ 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 = "~/git/mosaic_2020/output/stats/"
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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 = "~/git/mosaic_2020/output/plots/"
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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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@ -23,7 +23,7 @@ ifelse(!dir.exists(outdir_plots), dir.create(outdir_plots), FALSE)
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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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, fileEncoding = 'latin1')
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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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@ -42,4 +42,4 @@ metadata_all = all_df[, meta_data_cols]
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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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########################################################################
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########################################################################
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