VST {Seurat} | R Documentation |
Variance Stabilizing Transformation
Description
Apply variance stabilizing transformation for selection of variable features
Usage
VST(data, margin = 1L, nselect = 2000L, span = 0.3, clip = NULL, ...)
## Default S3 method:
VST(data, margin = 1L, nselect = 2000L, span = 0.3, clip = NULL, ...)
## S3 method for class 'IterableMatrix'
VST(
data,
margin = 1L,
nselect = 2000L,
span = 0.3,
clip = NULL,
verbose = TRUE,
...
)
## S3 method for class 'dgCMatrix'
VST(
data,
margin = 1L,
nselect = 2000L,
span = 0.3,
clip = NULL,
verbose = TRUE,
...
)
## S3 method for class 'matrix'
VST(data, margin = 1L, nselect = 2000L, span = 0.3, clip = NULL, ...)
Arguments
data |
A matrix-like object |
margin |
Unused |
nselect |
Number of of features to select |
span |
the parameter |
clip |
Upper bound for values post-standardization; defaults to the square root of the number of cells |
... |
Arguments passed to other methods |
verbose |
... |
Value
A data frame with the following columns:
-
“
mean
”: ... -
“
variance
”: ... -
“
variance.expected
”: ... -
“
variance.standardized
”: ... -
“
variable
”:TRUE
if the feature selected as variable, otherwiseFALSE
-
“
rank
”: If the feature is selected as variable, then how it compares to other variable features with lower ranks as more variable; otherwise,NA
[Package Seurat version 5.3.0 Index]