methFisherTest {methVisual} | R Documentation |
Fisher exact Test on two subsets of experiments over matched CpG sites
methFisherTest(methData,set1,set2)
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 |
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.
P- Values vector and a Plot
Arie Zackay <arie.zackay@mail.huji.ac.il>, Christine Steinhoff <steinhof@molgen.mpg.de>
data(methData) methFisherTest(methData,c(1,2,3),c(4,5,6))