added check_stats.R for non-severe analysis

2020-11-30 12:06:55 +00:00 · 2020-11-30 12:06:55 +00:00 · 6731b9484c
commit 6731b9484c
parent 37f8cd619e
1 changed files with 143 additions and 0 deletions
--- a/non_severe/check_stats.R
+++ b/non_severe/check_stats.R
@ -0,0 +1,143 @@
+#!/usr/bin/Rscript   
+getwd()
+setwd("~/git/mosaic_2020/")
+getwd()
+########################################################################
+# TASK: check stats
+########################################################################
+# load libraries, packages and local imports
+source("Header_TT.R")
+
+#=============
+# Input
+#=============
+source("data_extraction_mediators.R")
+source("read_data.R")
+
+########################################################################
+#=============
+# Data extraction for non-severe
+#=============
+table(fp_adults$T1_resp_score)
+table(fp_adults$obesity)
+
+df = fp_adults[fp_adults$T1_resp_score<3,]
+table(df$obesity)
+
+df_ob = df[df$obesity == 1,]
+df_nob = df[df$obesity == 0,]
+
+#============
+# npa
+#============
+# vl_pfu_ul: t2
+wilcox.test(df_ob$vl_pfu_ul_npa2, df_nob$vl_pfu_ul_npa2)
+wilcox_test(vl_pfu_ul_npa2 ~ obesity, data = df)
+
+foo = data.frame(df$obesity, df$vl_pfu_ul_npa2)
+na_c = sum(is.na(foo$df.vl_pfu_ul_npa2))
+nrow(df) - na_c
+
+
+# 1l29: t1
+wilcox.test(df_ob$il29_npa1, df_nob$il29_npa1)
+
+foo = data.frame(df$obesity, df$il29_npa1)
+na_c = sum(is.na(foo$df.il29_npa1))
+nrow(df) - na_c
+
+
+# tnfr1: t3
+wilcox.test(df_ob$tnfr1_npa3, df_nob$tnfr1_npa3)
+
+foo = data.frame(df$obesity, df$tnfr1_npa3)
+na_c = sum(is.na(foo$df.tnfr1_npa3))
+nrow(df) - na_c
+
+
+# rantes: t1
+wilcox.test(df_ob$rantes_npa1, df_nob$rantes_npa1)
+
+foo = data.frame(df$obesity, df$rantes_npa1)
+na_c = sum(is.na(foo$df.rantes_npa1))
+nrow(df) - na_c
+
+#============
+# sam
+#============
+# tarc: t3
+wilcox.test(df_ob$tarc_sam3
+            , df_nob$tarc_sam3)
+
+foo = data.frame(df$obesity, df$tarc_sam3)
+na_c = sum(is.na(foo$df.tarc_sam3))
+nrow(df) - na_c
+
+# il13: t3
+wilcox.test(df_ob$il13_sam3
+            , df_nob$il13_sam3)
+
+foo = data.frame(df$obesity, df$il13_sam3)
+na_c = sum(is.na(foo$df.il13_sam3))
+nrow(df) - na_c
+
+# eotaxin: t1
+wilcox.test(df_ob$eotaxin_sam1
+            , df_nob$eotaxin_sam1)
+
+foo = data.frame(df$obesity, df$eotaxin_sam1)
+na_c = sum(is.na(foo$df.eotaxin_sam1))
+nrow(df) - na_c
+
+
+#============
+# serum
+#============
+# ifna2a: t1
+wilcox.test(df_ob$ifna2a_serum1, 
+            df_nob$ifna2a_serum1)
+
+foo = data.frame(df$obesity, df$ifna2a_serum1)
+na_c = sum(is.na(foo$df.ifna2a_serum1))
+nrow(df) - na_c
+
+# mip17: t1
+wilcox.test(df_ob$mip17_serum1, 
+            df_nob$mip17_serum1)
+
+foo = data.frame(df$obesity, df$mip17_serum1)
+na_c = sum(is.na(foo$df.mip17_serum1))
+nrow(df) - na_c
+
+# il1: t1
+wilcox.test(df_ob$il1_serum1
+            , df_nob$il1_serum1)
+
+foo = data.frame(df$obesity, df$il1_serum1)
+na_c = sum(is.na(foo$df.il1_serum1))
+nrow(df) - na_c
+
+# ifna2a: t2 
+wilcox.test(df_ob$ifna2a_serum2, 
+            df_nob$ifna2a_serum2)
+
+foo = data.frame(df$obesity, df$ifna2a_serum2)
+na_c = sum(is.na(foo$df.ifna2a_serum2))
+nrow(df) - na_c
+
+# ifna2a: t3
+wilcox.test(df_ob$ifna2a_serum3, 
+            df_nob$ifna2a_serum3)
+
+foo = data.frame(df$obesity, df$ifna2a_serum3)
+na_c = sum(is.na(foo$df.ifna2a_serum3))
+nrow(df) - na_c
+
+# ifnb: t3
+wilcox.test(df_ob$ifnb_serum3
+            , df_nob$ifnb_serum3)
+
+foo = data.frame(df$obesity, df$ifnb_serum3)
+na_c = sum(is.na(foo$df.ifnb_serum3))
+nrow(df) - na_c
+