sage.test {sagenhaft} | R Documentation

## Compare Two SAGE Libraries

### Description

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

### Usage

    sage.test(x, y, n1=sum(x), n2=sum(y))

### Arguments

`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.

### Details

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.

### Value

Numeric vector of p-values.

### Author(s)

Gordon Smyth

### See Also

`fisher.test`

### Examples

    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

[Package sagenhaft version 1.0.0 Index]