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ran quick stats checks with wf data

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Tanushree Tunstall 2020-11-02 18:31:29 +00:00
parent f14c7ca64b
commit ba3c4564ea
1 changed files with 28 additions and 10 deletions
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38
stats_check.R
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@ -5,12 +5,12 @@
#============= #=============
# Input # Input
#============= #=============
source("data_extraction_formatting.R") source("plot_data.R")
#%%======================================================== #%%========================================================
# data assignment for stats # data assignment for stats
wf_npa = npa_df_adults_clean[npa_df_adults_clean$flustat == 1,] wf_npa = wf_fp_npa
wf_sam = sam_df_adults_clean[sam_df_adults_clean$flustat == 1,] wf_sam = wf_fp_sam
wf_serum = serum_df_adults_clean[serum_df_adults_clean$flustat == 1,] wf_serum = wf_fp_serum
############################################################ ############################################################
#========= #=========
# t1 # t1
@ -21,12 +21,18 @@ length(wf_npa$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$obesity == 0], paired = F) wilcox.test(wf_npa$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$il12p70_npa1)) length(wf_npa$il12p70_npa1) - sum(is.na(wf_npa$il12p70_npa1))
tapply(wf_npa$eotaxin3_npa1, wf_npa$obesity, mean, na.rm = T)
tapply(wf_npa$eotaxin3_npa1, wf_npa$obesity, median, na.rm = T)
#========= #=========
# t2 # t2
#========= #=========
wilcox.test(wf_npa$il4_npa2[wf_npa$obesity == 1], wf_npa$il4_npa2[wf_npa$obesity == 0], paired = F) wilcox.test(wf_npa$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$il4_npa2)) length(wf_npa$il4_npa2) - sum(is.na(wf_npa$il4_npa2))
tapply(wf_npa$il4_npa2, wf_npa$obesity, mean, na.rm = T)
tapply(wf_npa$il4_npa2, wf_npa$obesity, median, na.rm = T)
#========= #=========
# t3 # t3
#========= #=========
@ -45,11 +51,17 @@ length(wf_sam$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$obesity == 0], paired = F) wilcox.test(wf_sam$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$il12p70_sam1)) length(wf_sam$il12p70_sam1) - sum(is.na(wf_sam$il12p70_sam1))
tapply(wf_sam$il13_sam1, wf_sam$obesity, mean, na.rm = T)
tapply(wf_sam$il13_sam1, wf_sam$obesity, median, na.rm = T)
#========= #=========
# t2 # t2
#========= #=========
wilcox.test(wf_sam$il4_sam2[wf_sam$obesity == 1], wf_sam$il4_sam2[wf_sam$obesity == 0], paired = F) wilcox.test(wf_sam$il5_sam2[wf_sam$obesity == 1], wf_sam$il5_sam2[wf_sam$obesity == 0], paired = F)
length(wf_sam$il4_sam2) - sum(is.na(wf_sam$il4_sam2)) length(wf_sam$il5_sam2) - sum(is.na(wf_sam$il5_sam2))
tapply(wf_sam$il29_sam2, wf_sam$obesity, mean, na.rm = T)
tapply(wf_sam$il29_sam2, wf_sam$obesity, median, na.rm = T)
#========= #=========
# t3 # t3
@ -68,14 +80,17 @@ length(wf_sam$tnfr1_sam3) - sum(is.na(wf_sam$tnfr1_sam3))
wilcox.test(wf_serum$eotaxin3_serum1[wf_serum$obesity == 1], wf_serum$eotaxin3_serum1[wf_serum$obesity == 0], paired = F) wilcox.test(wf_serum$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$eotaxin3_serum1)) length(wf_serum$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$obesity == 0], paired = F) wilcox.test(wf_serum$neopterin_serum1[wf_serum$obesity == 1], wf_serum$neopterin_serum1[wf_serum$obesity == 0], paired = F)
length(wf_serum$ifna2a_serum1) - sum(is.na(wf_serum$ifna2a_serum1)) length(wf_serum$neopterin_serum1) - sum(is.na(wf_serum$neopterin_serum1))
tapply(wf_serum$eotaxin3_serum1, wf_serum$obesity, mean, na.rm = T)
tapply(wf_serum$eotaxin3_serum1, wf_serum$obesity, median, na.rm = T)
#========= #=========
# t2 # t2
#========= #=========
wilcox.test(wf_serum$il5_serum2[wf_serum$obesity == 1], wf_serum$il5_serum2[wf_serum$obesity == 0], paired = F) wilcox.test(wf_serum$il8_2_serum2[wf_serum$obesity == 1], wf_serum$il8_2_serum2[wf_serum$obesity == 0], paired = F)
length(wf_serum$il5_serum2) - sum(is.na(wf_serum$il5_serum2)) length(wf_serum$il8_2_serum2) - sum(is.na(wf_serum$il8_2_serum2))
#========= #=========
# t3 # t3
@ -83,3 +98,6 @@ length(wf_serum$il5_serum2) - sum(is.na(wf_serum$il5_serum2))
wilcox.test(wf_serum$rantes_serum3[wf_serum$obesity == 1], wf_serum$rantes_serum3[wf_serum$obesity == 0], paired = F) wilcox.test(wf_serum$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$rantes_serum3)) length(wf_serum$rantes_serum3) - sum(is.na(wf_serum$rantes_serum3))
tapply(wf_serum$itac_serum3, wf_serum$obesity, mean, na.rm = T)
tapply(wf_serum$itac_serum3, wf_serum$obesity, median, na.rm = T)