methFisherTest: Fisher exact Test on methylation Data

In methVisual: Methods for visualization and statistics on DNA methylation data

Description

Fisher exact Test on two subsets of experiments over matched CpG sites

Usage

methFisherTest(methData,set1,set2)

Arguments

methData	List; contains information on the pairwise alignments, and methylated CpG motifs.
set1	First subset - Integer vector of experiments due to there order at methData
set2	Second subset - Integer vector of indexes of experiments due to there order at methData

Details

Given two clone sequences groups A and B for each CpG site the user can investigate whether there is a difference of methylation status between the two groups at each of the CpG sites. In order to calculate this difference at each CpG site, the two-tailed p-value of Fisher's exact test is calculated from the 2*2 tables at each CpG site. This p-value indicates the level of difference at every single CpG in those two groups of clone sequences. A p-value smaller than 0.05 is an indication for the independence of the methylation state in a certain CpG site when comparing two groups of clone sequences.

Value

P- Values vector and a Plot

Author(s)

Arie Zackay <[e-mail]>, Christine Steinhoff <[e-mail]>

Examples

data(methData)
methFisherTest(methData,c(1,2,3),c(4,5,6))

methVisual documentation built on April 28, 2020, 7:08 p.m.