68 lines
2 KiB
R
Executable file
68 lines
2 KiB
R
Executable file
#!/usr/bin/Rscript
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getwd()
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setwd('~/git/covid_analysis/')
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getwd()
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############################################################
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# TASK: checking stats from manuscript
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############################################################
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# source data
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source("read_data.R")
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#%%========================================================
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# read file
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lf_data = read.csv(infile_icu_lf , stringsAsFactors = F)
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dim(lf_data)
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wf_data = read.csv(infile_icu_wf , stringsAsFactors = F)
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dim(wf_data)
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lf_t1 = lf_data[lf_data$timepoint == "t1",]
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lf_death_t1 = lf_t1[lf_t1$outcomes == 0,]
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lf_recovered_t1 = lf_t1[lf_t1$outcomes == 1,]
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wf_death = wf_data[wf_data$outcomes == 0,]
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wf_recovered = wf_data[wf_data$outcomes == 1,]
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kruskal.test(wf_death$Angiopoietin2_pgmL_t1, wf_death$Angiopoietin2_pgmL_t2, wf_death$Angiopoietin2_pgmL_t3)
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friedman.test(wf_death$Angiopoietin2_pgmL_t1, wf_recovered$Angiopoietin2_pgmL_t1)
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wilcox.test(wf_data$sRAGE_pgmL_t1, wf_data$sRAGE_pgmL_t3)
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# checks
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# sRAGE
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wilcox.test(wf$sRAGE_pgmL_t1, wf$sRAGE_pgmL_t3, paired = T) # 0.00039
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ks.test(wf_death$sRAGE_pgmL_t1, wf_death$sRAGE_pgmL_t2, wf_death$sRAGE_pgmL_t3)
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ks.test(wf_death$sRAGE_pgmL_t1, wf_death$sRAGE_pgmL_t3)
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wilcox.test(wf_death$sRAGE_pgmL_t1, wf_death$sRAGE_pgmL_t3, paired = T)
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summary(wf_death$sRAGE_pgmL_t1)
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ks.test(lf_death_t1$value[lf_death_t1$mediator == "sRAGE"]
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, lf_recovered_t1$value[lf_recovered_t1$mediator == "sRAGE"])
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#t1
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median(lf_t1$value[lf_t1$mediator == "sRAGE"])
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summary(lf_t1$value[lf_t1$mediator == "sRAGE"])
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# t2
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lf_t2 = lf_data[lf_data$timepoint == "t2",]
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median(lf_t2$value[lf_t2$mediator == "sRAGE"], na.rm = T)
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summary(lf_t2$value[lf_t2$mediator == "sRAGE"], na.rm = T)
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#t3
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lf_t3 = lf_data[lf_data$timepoint == "t3",]
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median(lf_t3$value[lf_t3$mediator == "sRAGE"], na.rm = T)
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summary(lf_t3$value[lf_t3$mediator == "sRAGE"], na.rm = T)
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# for trend
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lf_death = lf_data[lf_data$outcomes == 0,]
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lf_recovered = lf_data[lf_data$outcomes == 1,]
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ks.test(lf_death$value[lf_death$mediator == "sRAGE"]
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, lf_recovered$value[lf_recovered$mediator == "sRAGE"])
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