staged.build: create regulatory model of the gene, following all the...

In PriceLab/trenaSGM: trenaSGM: trena single gene model

Description

create regulatory model of the gene, following all the specified options, one stage at a time, saving intermedate data

Usage

## S4 method for signature 'FootprintDatabaseModelBuilder'
staged.build(obj, stage = c("find.footprints", "associateTFs", "build.models"))

Arguments

obj	An object of class FootprintDatabaseModelBuilder
stage	a character string, one of "find.footprints", "associateTFs", "build.models"
strategy	a list specifying all the options to build one or more models

Value

A list with two data.frames, "model" and "regulatoryRegions"

Examples

if(interactive()){
  fp.specs <- list(title="fp.2000up.200down",
                   type="database.footprints",
                   chrom="chr6",
                   tss=41163186,
                   start=(tss-2000),
                   downstream=(tss+200),
                   matrix
                   db.host="khaleesi.systemsbiology.net",
                   databases=list("brain_hint_20"),
                   motifDiscovery="builtinFimo",
                   tfMapping=c("TFClass", "MotifDB"),
                   tfPrefilterCorrelation=0.2)
  fpBuilder <- FootprintDatabaseModelBuilder("hg38", "TREM2", fp.specs, quiet=TRUE)
  load(system.file(package="trenaSGM", "extdata", "mayo.tcx.RData"))
  staged.build(fpBuilder, mtx, stage="find.footprints")
  }

PriceLab/trenaSGM documentation built on Oct. 5, 2020, 5:40 p.m.