ctest {exomePeak} | R Documentation

## ctest

### Description

c-test is used to compare two Poisson means, for peak calling or binding sites identification in exomePeak R-package

### Usage

    ctest(IP, INPUT, TOTAL_IP, TOTAL_INPUT, FOLD = 1, minimal_counts_in_fdr = 10)

### Arguments

`IP` | a vector of integers, each elemetnt represents the number of reads from a binding site in the IP sample
`INPUT` | a vector of integers, each elements represents the number of reads from a binding site in the Input control sample
`TOTAL_IP` | an integer, which represents the total number of reads in IP sample
`TOTAL_INPUT` | an integer, which represents the total number of reads in Input control sample
`FOLD` | a decimal number, which indicates the ration of Possion mean to be tested, default: 1. Use a larger number for detection of highly enriched binding sites.
`minimal_counts_in_fdr` | an integer threshold, only the loci with reads more than this number are subjected for fdr calculation. default: 10

### Details

c-test is used to compare two Poisson means, for peak calling or binding sites identification in exomePeak R-package. The comparison of two Possion distributions is converted into a binomial distribution based test. The number of reads at the same locus for the aligned reads are counted by other packages, such as Rsamtools or HTseq-count.

### Value

The function returns a list of length 3, which contains the log(p-value), log(fdr) and log(fold change), respectively.

### References

Przyborowski, J. and Wilenski, H. (1940) Homogeneity of results in testing samples from Poisson series: with an application to testing clover seed for dodder. Biometrika, 31, 313-323

### Examples

    result = ctest(c(20,10, 1), c(2,1,20), 100, 200)

[Package exomePeak version 2.13.2 Index]