BisRNA analyses non-conversion of bisulfite-treated RNA of a set of samples, in order to distinguish actual cytosine-5 methylation marks from artifacts. Calculations are done as follows:
each sample's ratio (Poisson parameter / coverage) is determined, assuming a null Poisson distribution (RNAmeth.poisson.par
),
non-conversion p-values are calculated for each sample (RNAmeth.poisson.test
),
combined non-conversion p-values and standard error of the non-conversion ratios
are calculated on the intersection of the set of samples samples.combine
.
A small non-conversion p-value points to methylation of a RNA cytosine, or another event blocking bisulfite conversion.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## Load data
data(Bisdata,package="BisRNA")
## Ratio (Poisson parameter / coverage), derived p-values,
# adjusted for multiple testing using either BH (here), or IHW if available.
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")
## Combined p-values ; median and standard error of
## bisulfite non-conversion ratio
BisXP.combined <- samples.combine(BisXP1,BisXP2,BisXP3)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.