runModelGeneVar: Calculate Variable Genes with Scran modelGeneVar

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Calculate Variable Genes with Scran modelGeneVar

Description

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.

Usage

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

Author(s)

Irzam Sarfraz

See Also

runFeatureSelection, runSeuratFindHVG, getTopHVG, plotTopHVG

Examples

data("scExample", package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- scaterlogNormCounts(sce, "logcounts")
sce <- runModelGeneVar(sce)
hvf <- getTopHVG(sce, method = "modelGeneVar", hvgNumber = 10,
          useFeatureSubset = NULL)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.