Description Usage Arguments Details Value Author(s) Examples

Mann Whitney U-Test on entire sets of CpG sites

1 | ```
methWhitneyUTest(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 |

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.

Returns a p-value

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

1 2 3 |

```
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
```

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.