sage.test: Compare Two SAGE Libraries In sagenhaft: Collection of functions for reading and comparing SAGE libraries

Description

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

Usage

 `1` ```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

`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 ```