VarianceFilter-class: Create a VarianceFilter object

In PriceLab/trena: Fit transcriptional regulatory networks using gene expression, priors, machine learning

Create a VarianceFilter object

Description

A VarianceFilter object allows for filtering based on the variance of a target gene in relation to other genes in the assay matrix. Using its associated getCandidates method, a VarianceFilter object can be used to filter a list of possible transcription factors to those within a given range of the variance of a supplied target gene.

Usage

VarianceFilter(mtx.assay = matrix(), targetGene, varSize = 0.5, quiet = TRUE)

Arguments

mtx.assay	An assay matrix of gene expression data
targetGene	A designated target gene that must be part of the mtx.assay data
varSize	A user-specified fraction (0-1) of the target gene variance to use as a filter
quiet	A logical denoting whether or not the solver should print output

Value

A CandidateFilter class object with variance as the filtering method

An object of the VarianceFilter class

See Also

getCandidates-VarianceFilter

Other Filtering Objects: FootprintFilter-class

Examples

load(system.file(package="trena", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
variance.filter <- VarianceFilter(mtx.assay = mtx.sub, targetGene = "MEF2C")

PriceLab/trena documentation built on March 16, 2023, 10:01 a.m.