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")
A SingleCellExperiment object
A character string to specify an assay to compute variable
features from. Default "logcounts"
.
inSCE
updated with variable feature metrics in rowData
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"