tanu/mosaic_2020
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separated checks from flu stats and added bonferrroni p

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This commit is contained in:
Tanushree Tunstall 2020-10-26 13:52:15 +00:00
parent 8e06f382c0
commit fe382dbf89
2 changed files with 62 additions and 47 deletions
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8
read_data.R
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@ -12,10 +12,10 @@ maindir = "~/git/mosaic_2020/"
outdir = paste0(maindir, "output/")
ifelse(!dir.exists(outdir), dir.create(outdir), FALSE)
outdir_stats = "~/git/mosaic_2020/output/stats/"
outdir_stats = paste0(maindir, "output/stats/")
ifelse(!dir.exists(outdir_stats), dir.create(outdir_stats), FALSE)
outdir_plots = "~/git/mosaic_2020/output/plots/"
outdir_plots = paste0(maindir, "output/plots")
ifelse(!dir.exists(outdir_plots), dir.create(outdir_plots), FALSE)
########################################################################
# static file read: csv
@ -23,7 +23,7 @@ ifelse(!dir.exists(outdir_plots), dir.create(outdir_plots), FALSE)
# all patients
#==============
all_df <- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mosaic_master_file_from_stata.csv"
, fileEncoding='latin1')
, fileEncoding = 'latin1')
# meta data columns
meta_data_cols = c("mosaic", "gender", "age", "adult", "flustat", "type"
@ -42,4 +42,4 @@ metadata_all = all_df[, meta_data_cols]
#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)
########################################################################
########################################################################