Normalize Data — NormalizeData • Seurat

Normalize the count data present in a given assay.

NormalizeData(object, ...)

# S3 method for default
NormalizeData(
  object,
  normalization.method = "LogNormalize",
  scale.factor = 10000,
  margin = 1,
  block.size = NULL,
  verbose = TRUE,
  ...
)

# S3 method for Assay
NormalizeData(
  object,
  normalization.method = "LogNormalize",
  scale.factor = 10000,
  margin = 1,
  verbose = TRUE,
  ...
)

# S3 method for Seurat
NormalizeData(
  object,
  assay = NULL,
  normalization.method = "LogNormalize",
  scale.factor = 10000,
  margin = 1,
  verbose = TRUE,
  ...
)

Arguments

object	An object
...	Arguments passed to other methods
normalization.method	Method for normalization. LogNormalize: Feature counts for each cell are divided by the total counts for that cell and multiplied by the scale.factor. This is then natural-log transformed using log1p. CLR: Applies a centered log ratio transformation RC: Relative counts. Feature counts for each cell are divided by the total counts for that cell and multiplied by the scale.factor. No log-transformation is applied. For counts per million (CPM) set `scale.factor = 1e6`
scale.factor	Sets the scale factor for cell-level normalization
margin	If performing CLR normalization, normalize across features (1) or cells (2)
block.size	How many cells should be run in each chunk, will try to split evenly across threads
verbose	display progress bar for normalization procedure
assay	Name of assay to use

Value

Returns object after normalization

Examples

if (FALSE) {
data("pbmc_small")
pbmc_small
pmbc_small <- NormalizeData(object = pbmc_small)
}