SCENIC (version 1.1.2-01)

geneFiltering: 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

# NOT RUN {
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)
# }