methWhitneyUTest: Mann Whitney U-Test on methylation data

Description Usage Arguments Details Value Author(s) Examples

View source: R/MethVisual.R

Description

Mann Whitney U-Test on entire sets of CpG sites

Usage

1

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

Mann Whitney U-Test (known also as wilcoxon-rank-sum test), is a non parametric test for assessing whether two independent samples of observations come from the same distribution. The null hypothesis in the Mann-Whitney U test is that the two samples are from a single population, which means that their probability distributions are equal. In the methVisual package the Mann-Whitney U test is applied in order to test if the distribution of methylated and non methylated sites in the profile under study between the given experimental sub groups of clone sequences is different. In order to calculate it, the two-tailed p-value of the Mann-Whitney U test is computed by ranking the ratios of methylated CpG sites to all CpG sites in a given clone sequence. The p-value in this case indicates if the distribution of ratio over all methylation states differ between the two groups.

Value

Returns a p-value

Author(s)

Arie Zackay <[email protected]>, Christine Steinhoff <[email protected]>

Examples

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## using methData
data(methData)
methWhitneyUTest(methData,c(1,2,3),c(4,5,6))

Example output

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, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

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
[1] 0.1314

methVisual documentation built on May 2, 2018, 2:49 a.m.