TrenaProject-class: TrenaProject

In PriceLab/TrenaProject: TrenaProject - an abstract base class for all projects

Description

TrenaProject and its (projected) subclasses provide convenient containers in which to collect trena-related aggregation of a gene's (a hierarchy of classes) including expression data, transcript and variant info, genomic and epigenomic context, trena models and/or the means to create them

Usage

TrenaProject(
  projectName,
  supportedGenes,
  genomeName,
  geneInfoTable.path,
  footprintDatabaseHost,
  footprintDatabaseNames,
  footprintDatabasePort = 5432,
  packageDataDirectory,
  quiet
)

Arguments

supportedGenes	a vector of character strings
footprintDatabaseHost	Character string (e.g., "khaleesi.systemsbiology.net")
footprintDatabaseNames	Character string (e.g., "hint_brain_20")
quiet	A logical indicating whether or not the Trena object should print output
expressionDirectory	A string pointing to a collection of RData expression matrices
genomicRegionsDirectory	A string pointing to a collection of RData files describing genomic regions of interest
variantsDirectory	A string pointing to a collection of RData variant files
covariatesFile	the (optional) name of a covariates files

Value

An object of the TrenaProject class

PriceLab/TrenaProject documentation built on April 3, 2020, 4:14 p.m.