bltest {exomePeak} | R Documentation

## bltest

### Description

This is the default test for the differential post-transcriptional RNA modification sites. Differential from all existing tests the compare the absolute amount between two conditions, this test compares whether the percentage of modified molecules are the same.

### Usage

    bltest(untreated_ip, untreated_input,
           treated_ip, treated_input,
           untreated_ip_total, untreated_input_total,
           treated_ip_total, treated_input_total,
           minimal_count_fdr =10)

### Arguments

`untreated_ip` | a vector of integers of n, which is the number of binding sites tested. Each element represents the number of reads fall into a binding site for the IP sample under untreated condition
`untreated_input` | a vector of integers of n, which is the number of binding sites tested. Each element represents the number of reads fall into a binding site for the Input control sample under untreated condition
`treated_ip` | a vector of integers of n, which is the number of binding sites tested. Each element represents the number of reads fall into a binding site for the IP sample under treated condition
`treated_input` | a vector of integers of n, which is the number of binding sites tested. Each element represents the number of reads fall into a binding site for the Input control sample under treated condition
`untreated_ip_total` | an integer, total number of reads for the IP sample under untreated condition
`untreated_input_total` | an integer, total number of reads for the Input control sample under untreated condition
`treated_ip_total` | an integer, total number of reads for the IP sample under treated condition
`treated_input_total` | an integer, total number of reads for the Input control sample under treated condition
`minimal_count_fdr` | an integer threshold, only the loci with reads more than this number are subjected for fdr calculation. default: 10

### Details

The comparison of 4 Poisson distributions are firstly collapsed into 2 Binomial distributions, and the function further tests whether the two binomial distributions have the same successful rate with a likelihood ratio 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, from the test.

### Author(s)

Lin Zhang, PhD <laurenie.zhang@gmail.com>

### References

Reference coming soon!

### Examples

    # input reads count of 3 binding sites
    untreated_ip = c(10,20,30)
    untreated_input = c(20,20,20)
    treated_ip = c(30,10,20)
    treated_input  = c(20,20,20)
    # sequencing depths
    untreated_ip_total = 10^7
    untreated_input_total = 10^7
    treated_ip_total = 10^7
    treated_input_total = 10^7
    # get the result
    result = bltest(untreated_ip, untreated_input,
    	treated_ip, treated_input,
    	untreated_ip_total, untreated_input_total,
    	treated_ip_total, treated_input_total)

[Package exomePeak version 2.16.0 Index]