getCandidates-VarianceFilter-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 'VarianceFilter'
getCandidates(obj, extraArgs)

Arguments

obj	An object of class VarianceFilter
extraArgs	A named list containing two fields: "target.gene" A designated target gene that should be part of the mtx.assay data "var.size" A user-specified percentage (0-1) of the target gene variance to use as a filter

Value

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

See Also

VarianceFilter

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

Examples

# Using the included Alzheimer's dataset, filter out only those transcription factors with variance
# within 50% of the variance of MEF2C
load(system.file(package="TReNA", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
variance.filter <- VarianceFilter(mtx.assay = mtx.sub)

target.gene <- "MEF2C"
tfs <- getCandidates(variance.filter, extraArgs = list("target.gene" = target.gene, "var.size" = 0.5))

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