exomePeak (version 2.6.0)

rhtest: rhtest

Description

This is the main 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

rhtest(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

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.

Details

The rhtest function is the main test used in exomePeak for comparing the transcription-independent dynamics in RNA epigenetic regulation between two experimental conditions. The sequencing depth from one condition is rescaled and the reads count from it is rescaled accordingly, so as to apply a hypergeometric test. The number of reads at a specific binding sites for the aligned reads are counted by other packages, such as Rsamtools or HTseq-count.

References

Meng, Jia, Xiaodong Cui, Manjeet K. Rao, Yidong Chen, and Yufei Huang. "Exome-based analysis for RNA epigenome sequencing data." Bioinformatics 29, no. 12 (2013): 1565-1567.

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 = rhtest(untreated_ip, untreated_input, 
	treated_ip, treated_input, 
	untreated_ip_total, untreated_input_total, 
	treated_ip_total, treated_input_total)