Calculate Variable Genes with Scran modelGeneVar

Generates and stores variability data in the input SingleCellExperiment object, using modelGeneVar method.

Also selects a specified number of top HVGs and store the logical selection in rowData.

runModelGeneVar(inSCE, useAssay = "logcounts")

Arguments

inSCE

A SingleCellExperiment object

useAssay

A character string to specify an assay to compute variable features from. Default "logcounts".

Value

inSCE updated with variable feature metrics in rowData

See also

runFeatureSelection, runSeuratFindHVG, getTopHVG, plotTopHVG

Author

Irzam Sarfraz

Examples

data("scExample", package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- scaterlogNormCounts(sce, "logcounts")
sce <- runModelGeneVar(sce)
getTopHVG(sce, method = "modelGeneVar", hvgNumber = 10)
#>  [1] "ENSG00000090382" "ENSG00000163220" "ENSG00000143546" "ENSG00000204287"
#>  [5] "ENSG00000019582" "ENSG00000101439" "ENSG00000011600" "ENSG00000196154"
#>  [9] "ENSG00000087086" "ENSG00000196126"