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

Description Usage Arguments Value Examples

tell us what we need to know

FootprintDatabaseModelBuilder(
  genomeName,
  targetGene,
  strategy,
  stagedExecutionDirectory = NA_character_,
  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 FootprintDatabaseModelBuilder class

if(interactive()){

  load(system.file(package="trenaSGM", "extdata", "mayo.tcx.RData"))
  fp.specs <- list(title="2000up.200down.fp",
                   type="database.footprints",
                   chrom="chr6",
                   tss=41163186,
                   upstream=2000,
                   downstream=200,
                   db.host="khaleesi.systemsbiology.net",
                   databases=list("brain_hint_16", "brain_hint_20", "brain_wellington_16", "brain_wellington_20"),
                   motifDiscovery="builtinFimo",
                   tfMapping=c("TFClass", "MotifDB"),
                   tfPrefilterCorrelation=0.2)
  fpc <- FootprintDatabaseModelBuilder("hg38", "TREM2", fp.specs)
  }