ScaleData: Scale and center the data.

Description

Scales and centers features in the dataset. If variables are provided in vars.to.regress, they are individually regressed against each feature, and the resulting residuals are then scaled and centered.

Usage

ScaleData(object, ...)
# S3 method for default
ScaleData(
  object,
  features = NULL,
  vars.to.regress = NULL,
  latent.data = NULL,
  split.by = NULL,
  model.use = "linear",
  use.umi = FALSE,
  do.scale = TRUE,
  do.center = TRUE,
  scale.max = 10,
  block.size = 1000,
  min.cells.to.block = 3000,
  verbose = TRUE,
  ...
)
# S3 method for IterableMatrix
ScaleData(
  object,
  features = NULL,
  do.scale = TRUE,
  do.center = TRUE,
  scale.max = 10,
  ...
)
# S3 method for Assay
ScaleData(
  object,
  features = NULL,
  vars.to.regress = NULL,
  latent.data = NULL,
  split.by = NULL,
  model.use = "linear",
  use.umi = FALSE,
  do.scale = TRUE,
  do.center = TRUE,
  scale.max = 10,
  block.size = 1000,
  min.cells.to.block = 3000,
  verbose = TRUE,
  ...
)
# S3 method for Seurat
ScaleData(
  object,
  features = NULL,
  assay = NULL,
  vars.to.regress = NULL,
  split.by = NULL,
  model.use = "linear",
  use.umi = FALSE,
  do.scale = TRUE,
  do.center = TRUE,
  scale.max = 10,
  block.size = 1000,
  min.cells.to.block = 3000,
  verbose = TRUE,
  ...
)

Arguments

object: An object
...: Arguments passed to other methods
features: Vector of features names to scale/center. Default is variable features.
vars.to.regress: Variables to regress out (previously latent.vars in RegressOut). For example, nUMI, or percent.mito.
latent.data: Extra data to regress out, should be cells x latent data
split.by: Name of variable in object metadata or a vector or factor defining grouping of cells. See argument f in split for more details
model.use: Use a linear model or generalized linear model (poisson, negative binomial) for the regression. Options are 'linear' (default), 'poisson', and 'negbinom'
use.umi: Regress on UMI count data. Default is FALSE for linear modeling, but automatically set to TRUE if model.use is 'negbinom' or 'poisson'
do.scale: Whether to scale the data.
do.center: Whether to center the data.
scale.max: Max value to return for scaled data. The default is 10. Setting this can help reduce the effects of features that are only expressed in a very small number of cells. If regressing out latent variables and using a non-linear model, the default is 50.
block.size: Default size for number of features to scale at in a single computation. Increasing block.size may speed up calculations but at an additional memory cost.
min.cells.to.block: If object contains fewer than this number of cells, don't block for scaling calculations.
verbose: Displays a progress bar for scaling procedure
assay: Name of Assay to scale

Details

ScaleData now incorporates the functionality of the function formerly known as RegressOut (which regressed out given the effects of provided variables and then scaled the residuals). To make use of the regression functionality, simply pass the variables you want to remove to the vars.to.regress parameter.

Setting center to TRUE will center the expression for each feature by subtracting the average expression for that feature. Setting scale to TRUE will scale the expression level for each feature by dividing the centered feature expression levels by their standard deviations if center is TRUE and by their root mean square otherwise.