added unpaired stats for asthma and severe for sam, serum and npa
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183
asthma/check_stats.R
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183
asthma/check_stats.R
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#!/usr/bin/Rscript
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getwd()
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setwd("~/git/mosaic_2020/")
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getwd()
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########################################################################
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# TASK: check stats
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########################################################################
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# load libraries, packages and local imports
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source("Header_TT.R")
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#=============
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# Input
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#=============
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source("data_extraction_mediators.R")
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#source("read_data.R")
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########################################################################
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#=============
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# Data extraction for non-severe
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#=============
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table(fp_adults_ics$asthma)
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table(fp_adults_ics$obesity)
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df = fp_adults_ics[fp_adults_ics$asthma == 1,]
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table(df$obesity)
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df_ob = df[df$obesity == 1,]
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df_nob = df[df$obesity == 0,]
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rm(npa_lf, npa_wf, sam_lf, sam_wf, serum_lf, serum_wf, fp_adults_ics)
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#============
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# npa
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#============
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# il8: t2
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wilcox.test(df_ob$il8_serum2, df_nob$il8_serum2)
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wilcox_test(il8_serum2 ~ obesity, data = df)
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foo = data.frame(df$obesity, df$il8_serum2)
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na_c = sum(is.na(foo$df.il8_serum2))
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nrow(df) - na_c
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tapply(df$il8_serum2, df$obesity, median, na.rm = T)
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tapply(df$il8_serum2, df$obesity, summary, na.rm = T)
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# il8_2: t2
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wilcox.test(df_ob$il8_2_serum2, df_nob$il8_2_serum2)
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wilcox_test(il8_2_serum2 ~ obesity, data = df)
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foo = data.frame(df$obesity, df$il8_2_serum2)
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na_c = sum(is.na(foo$df.il8_2_serum2))
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nrow(df) - na_c
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tapply(df$il8_2_serum2, df$obesity, median, na.rm = T)
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tapply(df$il8_2_serum2, df$obesity, summary, na.rm = T)
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# il4: t3
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wilcox.test(df_ob$il4_serum3, df_nob$il4_serum3)
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wilcox_test(il4_serum3 ~ obesity, data = df)
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foo = data.frame(df$obesity, df$il4_serum3)
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na_c = sum(is.na(foo$df.il4_serum3))
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nrow(df) - na_c
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tapply(df$il4_serum3, df$obesity, median, na.rm = T)
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tapply(df$il4_serum3, df$obesity, summary, na.rm = T)
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# ifnb: t3
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wilcox.test(df_ob$ifnb_serum3, df_nob$ifnb_serum3)
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wilcox_test(ifnb_serum3 ~ obesity, data = df)
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foo = data.frame(df$obesity, df$ifnb_serum3)
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na_c = sum(is.na(foo$df.ifnb_serum3))
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nrow(df) - na_c
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tapply(df$ifnb_serum3, df$obesity, median, na.rm = T)
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tapply(df$ifnb_serum3, df$obesity, summary, na.rm = T)
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#============
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# sam
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#============
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# tarc: t3
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wilcox.test(df_ob$tarc_sam3
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, df_nob$tarc_sam3)
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foo = data.frame(df$obesity, df$tarc_sam3)
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na_c = sum(is.na(foo$df.tarc_sam3))
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nrow(df) - na_c
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tapply(df$tarc_sam3, df$obesity, median, na.rm = T)
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# il13: t3
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wilcox.test(df_ob$il13_sam3
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, df_nob$il13_sam3)
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foo = data.frame(df$obesity, df$il13_sam3)
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na_c = sum(is.na(foo$df.il13_sam3))
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nrow(df) - na_c
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tapply(df$il13_sam3, df$obesity, median, na.rm = T)
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# eotaxin: t1
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wilcox.test(df_ob$eotaxin_sam1
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, df_nob$eotaxin_sam1)
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foo = data.frame(df$obesity, df$eotaxin_sam1)
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na_c = sum(is.na(foo$df.eotaxin_sam1))
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nrow(df) - na_c
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tapply(df$eotaxin_sam1, df$obesity, median, na.rm = T)
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#============
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# serum
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#============
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# ifna2a: t1
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wilcox.test(df_ob$ifna2a_serum1,
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df_nob$ifna2a_serum1)
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foo = data.frame(df$obesity, df$ifna2a_serum1)
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na_c = sum(is.na(foo$df.ifna2a_serum1))
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nrow(df) - na_c
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tapply(df$ifna2a_serum1, df$obesity, median, na.rm = T)
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# mip17: t1
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wilcox.test(df_ob$mip17_serum1,
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df_nob$mip17_serum1)
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foo = data.frame(df$obesity, df$mip17_serum1)
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na_c = sum(is.na(foo$df.mip17_serum1))
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nrow(df) - na_c
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tapply(df$mip17_serum1, df$obesity, median, na.rm = T)
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# il1: t1
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wilcox.test(df_ob$il1_serum1
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, df_nob$il1_serum1)
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foo = data.frame(df$obesity, df$il1_serum1)
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na_c = sum(is.na(foo$df.il1_serum1))
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nrow(df) - na_c
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tapply(df$il1_serum1, df$obesity, median, na.rm = T)
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tapply(df$il1_serum1, df$obesity, summary, na.rm = T)
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boxplot(df_ob$il1_serum1, df_nob$il1_serum1)
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# ifna2a: t2
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wilcox.test(df_ob$ifna2a_serum2,
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df_nob$ifna2a_serum2)
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foo = data.frame(df$obesity, df$ifna2a_serum2)
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na_c = sum(is.na(foo$df.ifna2a_serum2))
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nrow(df) - na_c
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tapply(df$ifna2a_serum2, df$obesity, median, na.rm = T)
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# ifna2a: t3
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wilcox.test(df_ob$ifna2a_serum3,
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df_nob$ifna2a_serum3)
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foo = data.frame(df$obesity, df$ifna2a_serum3)
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na_c = sum(is.na(foo$df.ifna2a_serum3))
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nrow(df) - na_c
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tapply(df$ifna2a_serum3, df$obesity, median, na.rm = T)
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# ifnb: t3
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wilcox.test(df_ob$ifnb_serum3
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, df_nob$ifnb_serum3)
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foo = data.frame(df$obesity, df$ifnb_serum3)
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na_c = sum(is.na(foo$df.ifnb_serum3))
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nrow(df) - na_c
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tapply(df$ifnb_serum3, df$obesity, median, na.rm = T)
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