regionBasedCoverage: regionBasedCoverage - transformation of the region coverage...
In rnaSeqMap: rnaSeq secondary analyses

Description Usage Arguments Value Author(s) Examples

The function builds a NucleotideDistr object from another object of coverage, using sequential call of Lindell-Aumann algorithm on the same data with a sequence of mi-levels. Each nucleotide is assigned the maximum mi-value of a region that covers it.

The output NucleotideDistr object has the distribution without peaks and small drops of coverage, but the thade-off is that the level of coverage are discrete: seq\*maxexp.

1	regionBasedCoverage(nd, seqq=1:10, maxexp=20, minsup=5)

`nd`	An object of `NucleotideDistr` class that has coverage values for a given region
`seqq`	Vector of numbers used to divide the range of coverage for subsequent mi-levels
`maxexp`	The maximal mi-level for coverage
`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 a maximum of mi-levels used for the sequential region searched. The distributions are similar to coverage, but have removed outliers of coverage peaks and short drops of 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 <- regionBasedCoverage(nd.cov, 1:10, 100)
  #runs the Lindell-Aumann algorithm at 100, 90, ... and picks maximal mi-level, where the nucleotide has a region found
#  }