RegionsMotifMatchingModelBuilder-class: Create a RegionsMotifMatchingModelBuilder object
In PriceLab/trenaSGM: trenaSGM: trena single gene model

Description Usage Arguments Value Examples

tell us what we need to know

RegionsMotifMatchingModelBuilder(
  genomeName,
  targetGene,
  strategy,
  quiet = TRUE
)

`genomeName`	hg38, mm10, ...
`targetGene`	in same vocabulary as rownames in the expression matrix
`quiet`	do or do not print progress information

An object of the RegionsMotifMatchingModelBuilder class

if(interactive()){

  load(system.file(package="trenaSGM", "extdata", "mayo.tcx.RData"))
  spec <- list(title="2000up.200down.rmm",
               type="regions.motifMatching",
               tss=41163186,
               regions=data.frame(chrom="chr6", start=41162986, end=41165186, stringsAsFactors=FALSE)
               matrix=mtx,
               motifDiscovery="matchPWM",
               matchThreshold=90,
               tfMapping=list("MotifDB"),
               tfPrefilterCorrelation=0.2)
  rmmBuilder <- RegionsMotifMatchingModelBuilder("hg38", "TREM2", spec)
  build(rmmBuilder)
  }