R/seuratFunctions.R
runSeuratFindHVG.Rd
runSeuratFindHVG Find highly variable genes and store in the input sce object
runSeuratFindHVG(
inSCE,
useAssay = "counts",
method = c("vst", "dispersion", "mean.var.plot"),
hvgNumber = 2000,
createFeatureSubset = "hvf",
altExp = FALSE,
verbose = TRUE
)
(sce) object to compute highly variable genes from and to store back to it
Specify the name of the assay to use for computation
of variable genes. It is recommended to use a raw counts assay with the
"vst"
method and normalized assay with all other methods. Default
is "counts"
.
selected method to use for computation of highly variable
genes. One of 'vst'
, 'dispersion'
, or 'mean.var.plot'
.
Default "vst"
which uses the raw counts. All other methods use
normalized counts.
numeric value of how many genes to select as highly
variable. Default 2000
Specify a name of the subset to create
for the identified variable features. Default is "hvf"
.
Leave it NULL
if you do not want to create a subset of
variable features.
Logical value indicating if the input object is an
altExperiment. Default FALSE
.
Logical value indicating if informative messages should
be displayed. Default is TRUE
.
Updated SingleCellExperiment
object with highly variable genes
computation stored
data(scExample, package = "singleCellTK")
sce <- runSeuratFindHVG(sce)
#> Sat Mar 18 10:31:26 2023 ... Feature subset variable 'hvf' created.