1. knitr::opts_chunk$set(warning = F, message = F)
  2. library(dplyr)
  3. library(tibble)

load phenotype

  1. phen <- read.csv("../../Result/phenotype/phenotype_20200111.csv")

group information

  1. with(phen, table(Group, Sex))

Sex

  1. with(phen, chisq.test(Group, Sex))

Age

  1. wilcox.test(Age ~ Group, data = phen)

other clincal parameters

  1. ncolumns <- c(1, 4, 13:ncol(phen))
  2. dat <- phen[, ncolumns] %>%
  3.   mutate(Group = factor(Group))
  4. datphen <- dat[, c(1:2)]
  5. datprof <- dat[, c(1, 3:ncol(dat))]
  7. fr <- levels(datphen$Group)
  8. res <- apply(datprof[, -1], 2, function(x, group){
  9.   df <- data.frame(Value=x, Group=group) %>% na.omit()
  10.   num <- as.numeric(table(df$Group))
  12.   pval <- t.test(Value ~ Group, data = df)$p.value
  13.   mn <- with(df, tapply(Value, Group, mean))
  14.   if ( mn[1] > mn[2]) {
  15.       enrich <- fr[1]
  16.   } else {
  17.       enrich <- fr[2]
  18.   }
  20.   sd <- with(df, tapply(Value, Group, sd))
  21.   mn_sd <- c(paste(signif(mn[1], 3), signif(sd[1], 3), sep = "+/-"),
  22.              paste(signif(mn[2], 3), signif(sd[2], 3), sep = "+/-"))
  23.   res <- c(pval, num, enrich, mn_sd)
  24.   return(res)
  25. }, datphen$Group) %>% 
  26.   t() %>% data.frame() %>%
  27.   setNames(c("Pvalue", paste0(fr, "_Number"), 
  28.              "Enrichment", paste0(fr, "_MeanSD"))) %>%
  29.   rownames_to_column("ClincalParam")
  31. DT::datatable(res)

version

  1. sessionInfo()