R Graphical Manual

Last data update: 2014.03.03

R: calculate the cutoff threshold of coverage

covThreshold

R Documentation

calculate the cutoff threshold of coverage

calculate the cutoff threshold of coverage for long form and short form

covThreshold(coverage, genome, txdb, utr3, 
                         chr="chr1", hugeData, groupList)

`coverage`	coverage for each sample, output of coverageFromBedGraph
`genome`	an object of BSgenome
`txdb`	an object of TxDb
`utr3`	output of utr3Annotation
`chr`	chromosome to be used for calculation, default is "chr1"
`hugeData`	is this dataset consume too much memory? if it is TRUE, the coverage will be saved into tempfiles.
`groupList`	group list of tag names