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

create regulatory model of the gene, following all the specified options

create regulatory model of the gene, following all the specified options

Usage

## S4 method for signature 'FootprintDatabaseModelBuilder'
build(obj)

## S4 method for signature 'RegionsMotifMatchingModelBuilder'
build(obj)

## S4 method for signature 'NoDnaModelBuilder'
build(obj)

Arguments

obj	An object of class NoDnaModelBuilder
strategy	a list specifying all the options to build one or more models

Value

A list with a bunch of tables...

A list with a bunch of tables...

A list with a bunch of tables...

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"))
  build(fpBuilder, mtx)
  }

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=list("TFClass", "MotifDB"),
                   tfPrefilterCorrelation=0.2)
  fpBuilder <- RegionsMotifMatchingModelBuilder("hg38", "TREM2", fp.specs, quiet=TRUE)
  load(system.file(package="trenaSGM", "extdata", "mayo.tcx.RData"))
  build(fpBuilder, mtx)
  }

if(interactive()){
  load(system.file(package="trenaSGM", "extdata", "mayo.tcx.RData"))
  build.spec <- list(title="trem2.noDNA.allTFs",
                     type="noDNA_tfsSupplied",
                     matrix=mtx,
                     tfPrefilterCorrelation=0.4,
                     orderByColumn="rfScore",
                     solverNames=c("lasso", "lassopv", "pearson", "randomForest", "ridge", "spearman"))

  builder <- NoDnaModelBuilder("hg38", "TREM2", build.spec, quiet=TRUE)
  build(builder)
  }

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