VarianceFilter-class.RdA 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.
VarianceFilter(mtx.assay = matrix(), targetGene, varSize = 0.5, quiet = TRUE)
| 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 |
A CandidateFilter class object with variance as the filtering method
An object of the VarianceFilter class
Other Filtering Objects:
FootprintFilter-class
load(system.file(package="trena", "extdata/ampAD.154genes.mef2cTFs.278samples.RData")) variance.filter <- VarianceFilter(mtx.assay = mtx.sub, targetGene = "MEF2C")