VarianceFilter-class {trena} | R Documentation

## 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")

[Package trena version 1.6.1 Index]