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

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/sagenhaft.R

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

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

`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

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