rnb.sample.summary.table {RnBeads} | R Documentation

## rnb.sample.summary.table

### Description

Creates a sample summary table from an RnBSet object

### Usage

    rnb.sample.summary.table(rnbSet)

### Arguments

`rnbSet` | `RnBSet` of interest.

### Value

a summary table (as data.frame) with the following variables for each sample (rows):

`sampleName` | Name of the sample
`*_num (* can be 'sites' or a region type)` | Number of sites or regions with coverage in the sample
`*_covgMean (`RnBiseqSet` only)` | Mean coverage of sites or regions in the sample
`*_covgMedian (`RnBiseqSet` only)` | Median coverage of sites or regions in the sample
`*_covgPerc25 (`RnBiseqSet` only)` | 25 percentile of coverage of sites or regions in the sample
`*_covgPerc75 (`RnBiseqSet` only)` | 75 percentile of coverage of sites or regions in the sample
`*_numCovg5,10,30,60 (`RnBiseqSet` only)` | Number of sites or regions with coverage greater or equal to 5,10,30,60
`sites_numDPval5em2,1em2,1em3 (`RnBeadSet` only)` | Number of sites with a detection p-value smaller than 0.05,0.01,0.001
`**_numSitesMean (** is any region type)` | Mean number of sites in a region
`**_numSitesMedian` | Median number of sites in a region
`**_numSites2,5,10,20` | Number of regions with at least 2,5,10,20 sites with valid methylation measurements

### Author(s)

Fabian Mueller

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    logger.start(fname=NA)
    rnb.sample.summary.table(rnb.set.example)

[Package RnBeads version 1.12.1 Index]