generators: Generators for synt data and
In rnaSeqMap: rnaSeq secondary analyses

Description Usage Arguments Author(s) Examples

Various generators for experiments.

generatorAddSquare(nd, deg, length.prop=0.5)
generatorAdd(nd, deg, length.prop=0.5)
generatorMultiply(nd, deg, length.prop=0.5)
generatorTrunc(nd,deg)
generatorSynth(nd, deg, length.prop=0.5)
generatorPeak(nd, deg, sr=10, mult=10)

`nd`	nucleotide distribution object
`deg`	degeneration level for the output profile
`length.prop`	a fraction of the genome region to be degenerated - (0,1)
`sr`	distance from the 5' end for the peak
`mult`	multiplier - how many times the peak is supposed to be higher than the maximum of the distribution

Generators of synthetic and semi-synthetic coverage profiles, for RNA-seq measures testing.

Anna Lesniewska,Michal Okoniewski

   if (1==0)
   {
   rs <- newSeqReads('chr2', 220238268, 220254744, -1)
   f <- c("test1.bam", "test2.bam", "test3.bam", "test4.bam", "test5.bam")
   ff <- sapply(f, function(x) system.file("extdata", x, package = "rnaSeqMap"))
   rs <- getBamData(rs, 1:5)    	 
   nd <- getCoverageFromRS(rs, 1:5) 
   generatorTrunc(nd,0.5)
   }