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added stats_check.R to cross check

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Tanushree Tunstall 2020-10-26 20:16:24 +00:00
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commit 6da0bd2e00
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stats_check.R Executable file
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#!/usr/bin/Rscript
############################################################
# TASK: to check unpaired stats from WF data
############################################################
#=============
# Input
#=============
source("data_extraction_formatting.R")
#%%========================================================
# data assignment for stats
wf_npa = npa_df_adults_clean[npa_df_adults_clean$flustat == 1,]
wf_sam = sam_df_adults_clean[sam_df_adults_clean$flustat == 1,]
wf_serum = serum_df_adults_clean[serum_df_adults_clean$flustat == 1,]
############################################################
#=========
# t1
#=========
wilcox.test(wf_npa$eotaxin3_npa1[wf_npa$obesity == 1], wf_npa$eotaxin3_npa1[wf_npa$obesity == 0], paired = F)
length(wf_npa$eotaxin3_npa1) - sum(is.na(wf_npa$eotaxin3_npa1))
wilcox.test(wf_npa$il12p70_npa1[wf_npa$obesity == 1], wf_npa$il12p70_npa1[wf_npa$obesity == 0], paired = F)
length(wf_npa$il12p70_npa1) - sum(is.na(wf_npa$il12p70_npa1))
#=========
# t2
#=========
wilcox.test(wf_npa$il4_npa2[wf_npa$obesity == 1], wf_npa$il4_npa2[wf_npa$obesity == 0], paired = F)
length(wf_npa$il4_npa2) - sum(is.na(wf_npa$il4_npa2))
#=========
# t3
#=========
wilcox.test(wf_npa$ip10_npa3[wf_npa$obesity == 1], wf_npa$ip10_npa3[wf_npa$obesity == 0], paired = F)
length(wf_npa$ip10_npa3) - sum(is.na(wf_npa$ip10_npa3))
###################################################################
##########
# sam
##########
#=========
# t1
#=========
wilcox.test(wf_sam$eotaxin3_sam1[wf_sam$obesity == 1], wf_sam$eotaxin3_sam1[wf_sam$obesity == 0], paired = F)
length(wf_sam$eotaxin3_sam1) - sum(is.na(wf_sam$eotaxin3_sam1))
wilcox.test(wf_sam$il12p70_sam1[wf_sam$obesity == 1], wf_sam$il12p70_sam1[wf_sam$obesity == 0], paired = F)
length(wf_sam$il12p70_sam1) - sum(is.na(wf_sam$il12p70_sam1))
#=========
# t2
#=========
wilcox.test(wf_sam$il4_sam2[wf_sam$obesity == 1], wf_sam$il4_sam2[wf_sam$obesity == 0], paired = F)
length(wf_sam$il4_sam2) - sum(is.na(wf_sam$il4_sam2))
#=========
# t3
#=========
wilcox.test(wf_sam$tnfr1_sam3[wf_sam$obesity == 1], wf_sam$tnfr1_sam3[wf_sam$obesity == 0], paired = F)
length(wf_sam$tnfr1_sam3) - sum(is.na(wf_sam$tnfr1_sam3))
###################################################################
##########
# serum
##########
#=========
# t1
#=========
wilcox.test(wf_serum$eotaxin3_serum1[wf_serum$obesity == 1], wf_serum$eotaxin3_serum1[wf_serum$obesity == 0], paired = F)
length(wf_serum$eotaxin3_serum1) - sum(is.na(wf_serum$eotaxin3_serum1))
wilcox.test(wf_serum$ifna2a_serum1[wf_serum$obesity == 1], wf_serum$ifna2a_serum1[wf_serum$obesity == 0], paired = F)
length(wf_serum$ifna2a_serum1) - sum(is.na(wf_serum$ifna2a_serum1))
#=========
# t2
#=========
wilcox.test(wf_serum$il5_serum2[wf_serum$obesity == 1], wf_serum$il5_serum2[wf_serum$obesity == 0], paired = F)
length(wf_serum$il5_serum2) - sum(is.na(wf_serum$il5_serum2))
#=========
# t3
#=========
wilcox.test(wf_serum$rantes_serum3[wf_serum$obesity == 1], wf_serum$rantes_serum3[wf_serum$obesity == 0], paired = F)
length(wf_serum$rantes_serum3) - sum(is.na(wf_serum$rantes_serum3))