Compute p-values for differential expression for each tag between two SAGE libraries.

1 |

`x` |
integer vector giving counts in first library. Non-integer values are rounded to the nearest integer. |

`y` |
integer vector giving counts in second library. Non-integer values are rounded to the nearest integer. |

`n1` |
total number of tags in first library. Non-integer values are rounded to the nearest integer. |

`n2` |
total number of tags in second library. Non-integer values are rounded to the nearest integer. |

This function uses a binomial approximation to the Fisher Exact test
for each tag. The approximation is accurate when `n1`

and
`n2`

are large and `x`

and `y`

are small in comparison.

Numeric vector of p-values.

Gordon Smyth

`fisher.test`

1 2 3 4 5 6 | ```
library(sagenhaft)
sage.test(c(0,5,10),c(0,30,50),n1=10000,n2=15000)
# Exact equivalents
fisher.test(matrix(c(0,0,10000-0,15000-0),2,2))$p.value
fisher.test(matrix(c(5,30,10000-5,15000-30),2,2))$p.value
fisher.test(matrix(c(10,50,10000-10,15000-50),2,2))$p.value
``` |

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.