samples.combine: Combine samples p-values and ratios

In BisRNA: Analysis of RNA Cytosine-5 Methylation

Description

samples.combine takes RNA bisulfite sequencing samples as input, combines their p-values using Fisher's method, and produces median and standard error of the bisulfite non-conversion ratios.

Usage

samples.combine(BisXP1, ...)

Arguments

BisXP1	A BisXP object containing non-conversion ratio and p-value
...	One or more additional samples, in the form of BisXP objects

Details

This function takes several bisulfite sequencing samples, in form of BisXP objects, as inputs. It is recommended to provide at least 3 samples and in any case all available, relevant samples. Using RNA and C positions present in all samples, the adjusted p-values of each sample are combined using Fisher's method. Median and standard error of the non-conversion ratio are also given in output.

Value

This function returns a data frame whose row names correspond to the RNA and C position which are present in all samples, and the following variables:

p.adj.combined

p-value adjusted (done in the preparation of the BisXP object) and combined (done here)

nonconv.ratio.med

Median of bisulfite non-conversion ratio for a specific RNA and C positions

nonconv.ratio.se

Standard error of bisulfite non-conversion ratio for a specific RNA and C positions

References

Fisher RA (1925) Statistical Methods for Research Workers. Edinburg: Oliver and Boyd.

Fisher RA (1948) Questions and Answers #14. In: Mosteller F, Fisher RA (1948) The American Statistician, 2:30-31 http://www.jstor.org/stable/2681650

Examples

 ## Load data
 data(Bisdata,package="BisRNA")

 ## Obtain the ratio (Poisson parameter / coverage), and p-values
 ## adjusted for multiple testing using BH (here) or IHW method.
 lambda1 <- RNAmeth.poisson.par(Bisdata1)$estimate
 BisXP1  <- RNAmeth.poisson.test(Bisdata1,lambda1,method="BH")
 lambda2 <- RNAmeth.poisson.par(Bisdata2)$estimate
 BisXP2  <- RNAmeth.poisson.test(Bisdata2,lambda2,method="BH")
 lambda3 <- RNAmeth.poisson.par(Bisdata3)$estimate
 BisXP3  <- RNAmeth.poisson.test(Bisdata3,lambda3,method="BH")

 ## Combine samples
 BisXP.combined <- samples.combine(BisXP1,BisXP2,BisXP3)

BisRNA documentation built on May 2, 2019, 2:35 a.m.