HVFInfo {SeuratObject} | R Documentation |
Get and set variable feature information for an Assay
object.
HVFInfo
and VariableFeatures
utilize generally variable
features, while SVFInfo
and SpatiallyVariableFeatures
are
restricted to spatially variable features
HVFInfo(object, method, status = FALSE, ...)
VariableFeatures(object, method = NULL, ...)
VariableFeatures(object, ...) <- value
SVFInfo(object, method, status, ...)
SpatiallyVariableFeatures(object, method, ...)
## S3 method for class 'Seurat'
HVFInfo(
object,
method = NULL,
status = FALSE,
assay = NULL,
selection.method = deprecated(),
...
)
## S3 method for class 'Seurat'
VariableFeatures(
object,
method = NULL,
assay = NULL,
nfeatures = NULL,
layer = NA,
simplify = TRUE,
selection.method = deprecated(),
...
)
## S3 replacement method for class 'Seurat'
VariableFeatures(object, assay = NULL, ...) <- value
## S3 method for class 'Seurat'
SVFInfo(
object,
method = c("markvariogram", "moransi"),
status = FALSE,
assay = NULL,
selection.method = deprecated(),
...
)
## S3 method for class 'Seurat'
SpatiallyVariableFeatures(
object,
method = "moransi",
assay = NULL,
decreasing = TRUE,
selection.method = deprecated(),
...
)
## S3 method for class 'Assay'
HVFInfo(object, method, status = FALSE, selection.method = deprecated(), ...)
## S3 method for class 'Assay'
SpatiallyVariableFeatures(
object,
method = "moransi",
decreasing = TRUE,
selection.method = deprecated(),
...
)
## S3 method for class 'Assay'
SVFInfo(
object,
method = c("markvariogram", "moransi"),
status = FALSE,
selection.method = deprecated(),
...
)
## S3 method for class 'Assay'
VariableFeatures(object, method = NULL, selection.method = deprecated(), ...)
## S3 replacement method for class 'Assay'
VariableFeatures(object, ...) <- value
## S3 method for class 'Assay5'
HVFInfo(object, method = NULL, status = FALSE, layer = NULL, strip = TRUE, ...)
## S3 method for class 'Assay5'
VariableFeatures(
object,
method = NULL,
layer = NA,
simplify = TRUE,
nfeatures = Inf,
selection.method = deprecated(),
...
)
## S3 replacement method for class 'Assay5'
VariableFeatures(object, method = "custom", layer = NULL, ...) <- value
object |
An object |
method |
Which method to pull. For
For
|
status |
Add variable status to the resulting data frame |
... |
Arguments passed to other methods |
value |
A character vector of variable features |
assay |
Name of assay to pull highly variable feature information for |
selection.method |
|
nfeatures |
Maximum number of features to select when simplifying |
layer |
Layer to pull variable features for |
simplify |
When pulling for multiple layers, combine into a single vector and select a common set of variable features for all layers |
decreasing |
Return features in decreasing order (most spatially variable first). |
strip |
Remove method/layer identifiers from highly variable data frame |
HVFInfo
: A data frame with feature means, dispersion, and
scaled dispersion
VariableFeatures
: a vector of the variable features
SVFInfo
: a data frame with the spatially variable features
SpatiallyVariableFeatures
: a character vector of the spatially
variable features
# Get the HVF info from a specific Assay in a Seurat object
HVFInfo(object = pbmc_small, assay = "RNA")[1:5, ]
# Get the HVF info directly from an Assay object
HVFInfo(pbmc_small[["RNA"]], method = 'vst')[1:5, ]