samples.combine function

Combine samples p-values and ratios

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.

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

Returns

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

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.

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)

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