getCandidates-FootprintFilter-method: Get candidate genes using the variance filter

In TReNA: Fit transcriptional regulatory networks using gene expression, priors, machine learning

Description

Get candidate genes using the variance filter

Usage

## S4 method for signature 'FootprintFilter'
getCandidates(obj, extraArgs)

Arguments

obj

An object of class FootprintFilter

extraArgs

A named list containing 5 fields: "target.gene" A designated target gene that should be part of the mtx.assay data "genome.db.uri" A connection to a genome database containing footprint information "project.db.uri" A connection to a project database containing footprint information "size.upstream" An integer denoting the distance upstream of the target gene to look for footprints "size.downstream" An integer denoting the distance downstream of the target gene to look for footprints

Value

A vector containing all genes with variances less than the target gene

See Also

FootprintFilter

Other getCandidate Methods: getCandidates,NullFilter-method, getCandidates,VarianceFilter-method, getCandidates

Examples

# Use footprint filter with the included SQLite database for MEF2C to filter candidates
# in the included Alzheimer's dataset
load(system.file(package="TReNA", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
footprint.filter <- FootprintFilter(mtx.assay = mtx.sub)

target.gene <- "MEF2C"
db.address <- system.file(package="TReNA", "extdata")
genome.db.uri <- paste("sqlite:/",db.address,"genome.sub.db", sep = "/")
project.db.uri <- paste("sqlite:/",db.address,"project.sub.db", sep = "/")

tfs <- getCandidates(footprint.filter, extraArgs = list("target.gene" = target.gene,
"genome.db.uri" = genome.db.uri, "project.db.uri" = project.db.uri,
"size.upstream" = 1000, "size.downstream" = 1000))

TReNA documentation built on Nov. 17, 2017, 12:35 p.m.