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.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
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'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> library(methVisual)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: XVector
Loading required package: plotrix
Loading required package: gsubfn
Loading required package: proto
Could not load tcltk. Will use slower R code instead.
Loading required package: grid
Loading required package: sqldf
Loading required package: RSQLite
Loading required package: DBI
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/methVisual/methFisherTest.Rd_%03d_medium.png", width=480, height=480)
> ### Name: methFisherTest
> ### Title: Fisher exact Test on methylation Data
> ### Aliases: methFisherTest
> ### Keywords: graphs
>
> ### ** Examples
>
> data(methData)
> methFisherTest(methData,c(1,2,3),c(4,5,6))
[1] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
[20] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.4 1.0 1.0 1.0 1.0 1.0
>
>
>
>
>
>
> dev.off()
null device
1
>