134 lines
4.7 KiB
R
Executable file
134 lines
4.7 KiB
R
Executable file
#!/usr/bin/Rscript
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############################################################
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# TASK: to check unpaired stats from WF data
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############################################################
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#=============
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# Input
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#=============
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source("plot_data.R")
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#%%========================================================
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# data assignment for stats
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wf_npa = wf_fp_npa
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wf_sam = wf_fp_sam
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wf_serum = wf_fp_serum
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############################################################
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# Numbers
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table(fp_adults_ics$asthma, fp_adults_ics$obesity)
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table(fp_adults_ics$obesity); table(fp_adults_ics$ia_cxr)
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table(fp_adults_ics$obesity, fp_adults_ics$ia_cxr)
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fisher.test(table(fp_adults_ics$obesity, fp_adults_ics$ia_cxr))
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table(fp_adults_ics$obesity, fp_adults_ics$com_noasthma)
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fisher.test(table(fp_adults_ics$obesity, fp_adults_ics$com_noasthma))
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chisq.test(table(fp_adults_ics$obesity, fp_adults_ics$com_noasthma))
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#=========
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# t1
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#=========
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wilcox.test(wf_npa$eotaxin3_npa1[wf_npa$obesity == 1], wf_npa$eotaxin3_npa1[wf_npa$obesity == 0], paired = F)
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length(wf_npa$eotaxin3_npa1) - sum(is.na(wf_npa$eotaxin3_npa1))
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wilcox.test(wf_npa$il12p70_npa1[wf_npa$obesity == 1], wf_npa$il12p70_npa1[wf_npa$obesity == 0], paired = F)
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length(wf_npa$il12p70_npa1) - sum(is.na(wf_npa$il12p70_npa1))
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tapply(wf_npa$eotaxin3_npa1, wf_npa$obesity, mean, na.rm = T)
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tapply(wf_npa$eotaxin3_npa1, wf_npa$obesity, median, na.rm = T)
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npa_wf_a = npa_wf[npa_wf$asthma == 1,]
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npa_wf_na = npa_wf[npa_wf$asthma == 0,]
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wilcox.test(npa_wf_a$il4_npa1[npa_wf_a$obesity == 1]
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, npa_wf_a$il4_npa1[npa_wf_a$obesity == 0], paired = F)
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length(npa_wf_a$il4_npa1) - sum(is.na(npa_wf_a$il4_npa1))
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wilcox.test(npa_wf_a$il13_npa1[npa_wf_a$obesity == 1]
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, npa_wf_a$il13_npa1[npa_wf_a$obesity == 0], paired = F)
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wilcox.test(npa_wf_na$il4_npa1[npa_wf_na$obesity == 1]
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, npa_wf_na$il4_npa1[npa_wf_na$obesity == 0], paired = F)
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wilcox.test(npa_wf_na$il13_npa1[npa_wf_na$obesity == 1]
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, npa_wf_na$il13_npa1[npa_wf_na$obesity == 0], paired = F)
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#=========
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# t2
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#=========
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wilcox.test(wf_npa$il4_npa2[wf_npa$obesity == 1], wf_npa$il4_npa2[wf_npa$obesity == 0], paired = F)
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length(wf_npa$il4_npa2) - sum(is.na(wf_npa$il4_npa2))
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tapply(wf_npa$il4_npa2, wf_npa$obesity, mean, na.rm = T)
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tapply(wf_npa$il4_npa2, wf_npa$obesity, median, na.rm = T)
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#=========
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# t3
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#=========
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wilcox.test(wf_npa$ip10_npa3[wf_npa$obesity == 1], wf_npa$ip10_npa3[wf_npa$obesity == 0], paired = F)
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length(wf_npa$ip10_npa3) - sum(is.na(wf_npa$ip10_npa3))
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###################################################################
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##########
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# sam
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##########
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#=========
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# t1
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#=========
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wilcox.test(wf_sam$eotaxin3_sam1[wf_sam$obesity == 1], wf_sam$eotaxin3_sam1[wf_sam$obesity == 0], paired = F)
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length(wf_sam$eotaxin3_sam1) - sum(is.na(wf_sam$eotaxin3_sam1))
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wilcox.test(wf_sam$il12p70_sam1[wf_sam$obesity == 1], wf_sam$il12p70_sam1[wf_sam$obesity == 0], paired = F)
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length(wf_sam$il12p70_sam1) - sum(is.na(wf_sam$il12p70_sam1))
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tapply(wf_sam$il13_sam1, wf_sam$obesity, mean, na.rm = T)
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tapply(wf_sam$il13_sam1, wf_sam$obesity, median, na.rm = T)
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#=========
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# t2
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#=========
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wilcox.test(wf_sam$il5_sam2[wf_sam$obesity == 1], wf_sam$il5_sam2[wf_sam$obesity == 0], paired = F)
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length(wf_sam$il5_sam2) - sum(is.na(wf_sam$il5_sam2))
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tapply(wf_sam$il29_sam2, wf_sam$obesity, mean, na.rm = T)
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tapply(wf_sam$il29_sam2, wf_sam$obesity, median, na.rm = T)
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#=========
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# t3
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#=========
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wilcox.test(wf_sam$tnfr1_sam3[wf_sam$obesity == 1], wf_sam$tnfr1_sam3[wf_sam$obesity == 0], paired = F)
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length(wf_sam$tnfr1_sam3) - sum(is.na(wf_sam$tnfr1_sam3))
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###################################################################
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##########
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# serum
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##########
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#=========
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# t1
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#=========
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wilcox.test(wf_serum$eotaxin3_serum1[wf_serum$obesity == 1], wf_serum$eotaxin3_serum1[wf_serum$obesity == 0], paired = F)
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length(wf_serum$eotaxin3_serum1) - sum(is.na(wf_serum$eotaxin3_serum1))
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wilcox.test(wf_serum$neopterin_serum1[wf_serum$obesity == 1], wf_serum$neopterin_serum1[wf_serum$obesity == 0], paired = F)
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length(wf_serum$neopterin_serum1) - sum(is.na(wf_serum$neopterin_serum1))
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tapply(wf_serum$eotaxin3_serum1, wf_serum$obesity, mean, na.rm = T)
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tapply(wf_serum$eotaxin3_serum1, wf_serum$obesity, median, na.rm = T)
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#=========
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# t2
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#=========
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wilcox.test(wf_serum$il8_2_serum2[wf_serum$obesity == 1], wf_serum$il8_2_serum2[wf_serum$obesity == 0], paired = F)
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length(wf_serum$il8_2_serum2) - sum(is.na(wf_serum$il8_2_serum2))
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#=========
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# t3
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#=========
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wilcox.test(wf_serum$rantes_serum3[wf_serum$obesity == 1], wf_serum$rantes_serum3[wf_serum$obesity == 0], paired = F)
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length(wf_serum$rantes_serum3) - sum(is.na(wf_serum$rantes_serum3))
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tapply(wf_serum$itac_serum3, wf_serum$obesity, mean, na.rm = T)
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tapply(wf_serum$itac_serum3, wf_serum$obesity, median, na.rm = T)
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