rnb.sample.summary.table: rnb.sample.summary.table

In RnBeads: RnBeads

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)

RnBeads documentation built on March 3, 2021, 2 a.m.