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

Description Usage Arguments Value Author(s) Examples

View source: R/NDtransforms.R View source: R/NucleotideDistr.R

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	findRegionsAsND(nd, mi, minsup=5)

`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

NucleotideDistr object that includes a matrix with zeros where no region was found and the value of mi for all the nucleotides included in the region. The type fo the object is "REG".

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)
#  }