rnb.sample.summary.table {RnBeads} | R Documentation |
Creates a sample summary table from an RnBSet object
rnb.sample.summary.table(rnbSet)
rnbSet |
|
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 ( |
Mean coverage of sites or regions in the sample |
*_covgMedian ( |
Median coverage of sites or regions in the sample |
*_covgPerc25 ( |
25 percentile of coverage of sites or regions in the sample |
*_covgPerc75 ( |
75 percentile of coverage of sites or regions in the sample |
*_numCovg5,10,30,60 ( |
Number of sites or regions with coverage greater or equal to 5,10,30,60 |
sites_numDPval5em2,1em2,1em3 ( |
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 |
Fabian Mueller
library(RnBeads.hg19) data(small.example.object) logger.start(fname=NA) rnb.sample.summary.table(rnb.set.example)