geneFiltering: geneFiltering

In aertslab/SCENIC: SCENIC (Single Cell rEgulatory Network Inference and Clustering)

geneFiltering

Description

Gene filtering

Usage

geneFiltering(
  exprMat,
  scenicOptions,
  minCountsPerGene = 3 * 0.01 * ncol(exprMat),
  minSamples = ncol(exprMat) * 0.01
)

Arguments

exprMat	Expression matrix
scenicOptions	scenicOptions object (slots used: RcisTarget databases and genesKept)
minCountsPerGene	Minimum counts per gene required
minSamples	Minimum number of samples (cells) in which the gene should be detected

Examples

setwd("SCENIC_MouseBrain")
scenicOptions <- readRDS("int/scenicOptions.Rds")

loomPath <- system.file(package="SCENIC", "examples/mouseBrain_toy.loom")
exprMat <- SCopeLoomR::get_dgem(SCopeLoomR::open_loom(loomPath))

genesKept <- geneFiltering(exprMat, scenicOptions=scenicOptions,
                           minCountsPerGene=3*.01*ncol(exprMat),
                           minSamples=ncol(exprMat)*.01)
overrideOptions <- list(dbFilePath="databases/mm9-500bp-upstream-7species.mc9nr.feather", outFile_genesKept=NULL)

aertslab/SCENIC documentation built on April 7, 2024, 10 a.m.