diff --git a/non_severe/check_stats.R b/non_severe/check_stats.R new file mode 100755 index 0000000..fa75589 --- /dev/null +++ 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 +