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

Description Usage Arguments Value See Also Examples

Description

Get candidate genes using the variance filter

Usage

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## 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

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# 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.