fastFET: Fast version of Fisher Exact Test
In MaayanLab/genesetr: Manipulate, Test, and Visualize Gene Set Overlaps

Description Usage Arguments Value Examples

Quickly compute FET p-values for n 2x2 contingency tables T = {t_1,t_2,...,t_n-1,t_n}

1	fastFET(a, b, c, d, alternative = "greater")

`a`	A vector of values where a_i corresponds to t_i
`b`	A vector of values where b_i corresponds to t_i
`c`	A vector of values where c_i corresponds to t_i
`d`	A vector of values where d_i corresponds to t_i

A vector of p-values P=p_1, p_2,...,p_n-1,p_n where p_i corresponds to the FET result of t_i.

T = \{t_{1},t_{2},...,t_{n-1},t_{n}\}, with each t_i of the form:
           setAn ¬setA
       setB  a     b | a+b
      ¬setB  c     d | c+d
         ------------|-----
            a+c   b+d| a+b+c+d

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)