batch_chisq_test_pvalue_calculator.r

library(readxl)
library(dplyr)

ARDS_COMPARE <- read_excel("D:/Desktop/ARDS_COMPARE.xlsx")
colnames(ARDS_COMPARE) <- c("compare", "number", "gene", "snp", "minor_allele_1", "major_allele_1", "minor_allele_2", "major_allele_2")

d <- ARDS_COMPARE %>% select(minor_allele_1, major_allele_1, minor_allele_2, major_allele_2)
d$minor_allele_1 = as.integer(d$minor_allele_1)
d$major_allele_1 = as.integer(d$major_allele_1)
d$minor_allele_2 = as.integer(d$minor_allele_2)
d$major_allele_2 = as.integer(d$major_allele_2)


calc_chisq_test_pvalue = function(row) {
  row = as.list(row)
  ct = chisq.test(matrix(c(row$minor_allele_1, row$major_allele_1, row$minor_allele_2, row$major_allele_2), byrow=FALSE, nrow=2))
  ct$p.value
}

ARDS_COMPARE$pvalue = apply(d, 1, calc_chisq_test_pvalue)
write.csv(ARDS_COMPARE, file="wujingzi.csv")