RNAmeth.poisson.test {BisRNA}

Test RNA Cytosine methylation based on Poisson model distribution

Description

RNAmeth.poisson.test tests RNA bisulfite sequencing non-conversion based on a sample and the ratio (Poisson parameter / coverage) for this sample.

Usage

RNAmeth.poisson.test(BisRNA, lambda, method="BH")

Arguments

BisRNA

A dataframe containing RNA name, C position, coverage and non-conversion ratio

lambda

Ratio (Poisson parameter / coverage)

method

Adjustment method for multiple testing, either "BH" (Benjamini-Hochberg) or "IHW" (Independent Hypothesis Weighting, from R package IHW)

Details

This function takes RNA bisulfite sequencing data from one sample and the ratio (Poisson parameter / coverage) as inputs. Then, the dataset is restricted to those C positions where non-conversion ratio is larger than (Poisson parameter / coverage). Finally, it carries out poisson.test and a correction for multiple testing. The output of function RNAmeth.poisson.test is a BisXP object which contains RNA names, C positions, non-conversion ratios and adjusted p-values. The formatting into a BisXP object guarantees that some consistency checks are satisfied.

Value

This function returns a BisXP object whose elements correspond to RNAs where non-conversion ratio is higher than lambda = ratio (Poisson parameter / coverage). The variables contained in this object are the non-conversion ratio and the adjusted p-value.

Examples

 ## Load data, find out ratio Poison parameter / coverage,
 ## and produce corresponding adjusted p-values.
 data(Bisdata,package="BisRNA")
 lambda1 <- RNAmeth.poisson.par(Bisdata1)$estimate
 BisXP1  <- RNAmeth.poisson.test(Bisdata1,lambda1,method="BH")

 ## Print BisXP1
 BisXP1

 ## Display BisXP1 as a data frame
 BisXP1.df <- data.frame(BisXP1$nonconv.ratio, BisXP1$pv.adj, row.names=BisXP1$RNA.pos)
 BisXP1.df