regionBasedCoverage {rnaSeqMap} | R Documentation |
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.
regionBasedCoverage(nd, seqq=1:10, maxexp=20, minsup=5)
nd |
An object of |
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 # }