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added stats for flu subjects only sam, serum & npa

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Tanushree Tunstall 2020-10-24 23:10:49 +01:00
parent 87559ea021
commit 69e8ac0ea8
4 changed files with 932 additions and 0 deletions
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test_flu_counts.R Normal file
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#!/usr/bin/Rscript
getwd()
setwd("~/git/mosaic_2020/")
getwd()
############################################################
# TASK: unpaired (time) analysis of mediators: SAM
############################################################
#=============
# Input
#=============
source("data_extraction_formatting.R")
#%%========================================================
# data assignment for stats
wf = sam_df_adults_clean[sam_df_adults_clean$flustat == 1,]
lf = sam_adults_lf[sam_adults_lf$flustat == 1,]
#%%========================================================
table(metadata_all$flustat[metadata_all$adult == 1])
aki_flu = read.csv(file.choose())
aki_flu_sub = unique(aki_flu$Subject.ID)
aki_flu_sub%in%wf$mosaic
sub_mis = wf$mosaic[!wf$mosaic%in%aki_flu_sub]; sub_mis
check = wf[wf$mosaic == sub_mis,]
check2 = wf[wf$age>=18,] #!hmmm