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Wrapper superfast version of Fisher Exact Test. This is the fastest implementation currently available. Uses phyper inside. Original code from 'corpora' R package

Source: R/fastFET.R
phyper.fastFET.Rd

       setAn ¬setA
   setB  a     b | a+b
  ¬setB  c     d | c+d
     ------------|-----
        a+c   b+d| a+b+c+d

Usage

phyper.fastFET(
  a,
  b,
  c,
  d,
  alternative = c("two.sided", "less", "greater")[3],
  log.p = FALSE
)

Details

Example: Given three contingency tables: setA ¬setA setA ¬setA setB ¬setB setB 3 100 setC 5 6 setD 20 45 ¬setB 123 500 ¬setC 10 100 ¬setD 60 1000

a=c(3, 5, 20) b=c(100, 6, 45) c=c(123, 10, 60) d=c(500, 100, 1000) pvals = fastFET(a,b,c,d)