Extracts or select the top variable genes from an input
SingleCellExperiment object. Note that the variability metrics
must be computed using the runFeatureSelection
method before
extracting the feature names of the top variable features. getTopHVG
only returns a character vector of the HVG selection, while with
setTopHVG
, a logical vector of the selection will be saved in the
rowData
, and optionally, a subset object for the HVGs can be stored
in the altExps
slot at the same time.
getTopHVG(
inSCE,
method = c("vst", "dispersion", "mean.var.plot", "modelGeneVar", "seurat", "seurat_v3",
"cell_ranger"),
hvgNumber = 2000,
useFeatureSubset = NULL,
featureDisplay = metadata(inSCE)$featureDisplay
)
setTopHVG(
inSCE,
method = c("vst", "dispersion", "mean.var.plot", "modelGeneVar", "seurat", "seurat_v3",
"cell_ranger"),
hvgNumber = 2000,
featureSubsetName = NULL,
genes = NULL,
genesBy = NULL,
altExp = FALSE
)
Input SingleCellExperiment object
Specify which method to use for variable gene extraction
from Seurat "vst"
, "mean.var.plot"
, "dispersion"
or
Scran "modelGeneVar"
or Scanpy "seurat"
, "cell_ranger"
,
"seurat_v3"
. Default "vst"
Specify the number of top variable genes to extract.
Get the feature names in the HVG list set by
setTopHVG
. Will ignore method
and hvgNumber
if not
NULL
. Default NULL
.
A character string for the rowData
variable name
to indicate what type of feature ID should be displayed. If set by
setSCTKDisplayRow
, will by default use it. If NULL
, will
use rownames(inSCE)
.
A character string for the rowData
variable
name to store a logical index of selected features. Default NULL
, will
be determined basing on other parameters.
A customized character vector of gene list to be set as a
rowData
variable. Will ignore method
and hvgNumber
if
set. Default NULL
.
If setting customized genes
, where should it be found
in rowData
? Leave NULL
for matching rownames
. Default
NULL
.
TRUE
for also creating a subset inSCE
object with
the selected HVGs and store this subset in the altExps
slot, named by
hvgListName
. Default FALSE
.
A character vector of the top hvgNumber
variable
feature names
The input inSCE
object with the logical vector of
HVG selection updated in rowData
, and related parameter updated in
metadata
. If altExp
is TRUE
, an altExp
is also
added
data("scExample", package = "singleCellTK")
sce <- runSeuratFindHVG(sce)
#> Sat Mar 18 10:27:57 2023 ... Feature subset variable 'hvf' created.
hvgs <- getTopHVG(sce, hvgNumber = 10)
sce <- setTopHVG(sce, method = "vst", hvgNumber = 5)
#> Sat Mar 18 10:27:57 2023 ... Feature subset variable 'HVG_vst5' created.