R语言Fisher精确检验

Fisher's Exact Test for Count Data

Description

Performs Fisher's exact test for testing the null of independence of rows and columns in a contingency table with fixed marginals.

Usage

fisher.test(x, y = NULL, workspace = 200000, hybrid = FALSE,
            hybridPars = c(expect = 5, percent = 80, Emin = 1),
            control = list(), or = 1, alternative = "two.sided",
            conf.int = TRUE, conf.level = 0.95,
            simulate.p.value = FALSE, B = 2000)

?fisher.test

Convictions <- matrix(c(2, 10, 15, 3), nrow = 2,
                      dimnames =
                        list(c("Dizygotic", "Monozygotic"),
                             c("Convicted", "Not convicted")))
Convictions
fisher.test(Convictions, alternative = "less")

Job <- matrix(c(1,2,1,0, 3,3,6,1, 10,10,14,9, 6,7,12,11), 4, 4,
              dimnames = list(income = c("< 15k", "15-25k", "25-40k", "> 40k"),
                              satisfaction = c("VeryD", "LittleD", "ModerateS", "VeryS")))
fisher.test(Job) # 0.7827

comp_result_df1$adjPval[1:5]

# 行为样品名，列为各个信号通路的突变情况（0:无突变，1:有突变）
mutMat <- as.matrix(tcga_crc_m0_GAM_pl_df) 

fisher.test(mutMat[,3],mutMat[,4])
# 等于
fisher.test(table(mutMat[,3],mutMat[,4]))
# fisher.test一般需要列联表中某一格小于5
# 结果和卡方检验差异不大
chisq.test(table(mutMat[,3],mutMat[,4]))