findRegionsAsIR: findRegionsAsIR - finding regions of high coverage using...
In rnaSeqMap: rnaSeq secondary analyses

Description Usage Arguments Value Author(s) Examples

The function is running Lindell-Aumann algorithm to find regions of irreducible expression on the coverage data in the NucleotideDistr object. The function may be used to find the location and boundaries of significant expression of exons and small RNA.

1	findRegionsAsIR(nd, mi, minsup=5, exp)

`nd`	An object of `NucleotideDistr` class that has coverage values for a given region
`mi`	The threshold of coverage that makes the region significant
`minsup`	Minimal support of the numeric association rule - namely, in this case, the mininmal length of the discovered region
`exp`	Sample (experiment) number

IRanges object with irreducible regions with high coverage.

Michal Okoniewski, Anna Lesniewska

#  if (xmapConnected())  
#  {
#    rs <- newSeqReads(1,1,20000,1)
#    rs <- addExperimentsToReadset(rs,1:3)
#    nd.cov <- getCoverageFromRS(rs,1:3)
#    nd.regs <- findRegionsAsND(nd.cov, 10)
#  }