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BisRNA (version 0.2.2)

Analysis of RNA Cytosine-5 Methylation

Description

Bisulfite-treated RNA non-conversion in a set of samples is analysed as follows : each sample's non-conversion distribution is identified to a Poisson distribution. P-values adjusted for multiple testing are calculated in each sample. Combined non-conversion P-values and standard errors are calculated on the intersection of the set of samples. For further details, see C Legrand, F Tuorto, M Hartmann, R Liebers, D Jakob, M Helm and F Lyko (2017) .

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Version

Install

install.packages('BisRNA')

Monthly Downloads

241

Version

0.2.2

License

GPL (>= 2)

Maintainer

Carine Legrand

Last Published

December 15th, 2017

Functions in BisRNA (0.2.2)

Bisdata3

Synthetic sample 3 of RNA bisulfite sequencing
Bisdata

Three synthetic samples of RNA bisulfite sequencing for examples and tests
RNAmeth.poisson.par

Find ratio (Poisson parameter / coverage) for one sample of bisulfite-converted RNA
read.BisXP

Read RNA bisulfite experiment data and cast it into a BisXP object
RNAmeth.poisson.test

Test RNA Cytosine methylation based on Poisson model distribution
fisher.method

Function implementing Fisher's method to combine independent p-values
samples.combine

Combine samples p-values and ratios
intersectMatrix

Take intersection of 2 tables
class.BisXP

Cast bisulfite experiment data into a BisXP object
BisRNA-package

Analysis of RNA Cytosine-5 Methylation from bisulfite sequencing experiments
testMeth

Apply poisson.test to BS coverage and non-conversion ratio.
Bisdata2

Synthetic sample 2 of RNA bisulfite sequencing
Bisdata1

Synthetic sample 1 of RNA bisulfite sequencing