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Last data update: 2014.03.03

R: regionBasedCoverage - transformation of the region coverage...

regionBasedCoverage

R Documentation

regionBasedCoverage - transformation of the region coverage by the Lindell-Aumann regions

Description

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.

Usage

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

Arguments

`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

Value

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.

Author(s)

Michal Okoniewski, Anna Lesniewska

Examples

#  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
#  }