FootprintFilter-class: Create a FootprintFilter object

In TReNA: Fit transcriptional regulatory networks using gene expression, priors, machine learning

Description

A FootprintFilter object allows for filtering based on gene footprinting databases. Using its associated getCandidates method and URIs for both a genome database and project database, a FootprintFilter object can be used to filter a list of possible transcription factors to those that match footprint motifs for a supplied target gene.

Usage

FootprintFilter(mtx.assay = matrix(), quiet = TRUE)

Arguments

mtx.assay	An assay matrix of gene expression data
quiet	A logical denoting whether or not the filter should print output

Value

An object of the FootprintFilter class

See Also

getCandidates-FootprintFilter, getFilterAssayData

Other Filtering Objects: NullFilter-class, VarianceFilter-class

Examples

load(system.file(package="TReNA", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
footprint.filter <- FootprintFilter(mtx.assay = mtx.sub)

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