RnBeads (version 1.4.0)

rnb.sample.summary.table: 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

Examples

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