Normalize MPX data — NormalizeMPX • pixelatorR

This function has been replaced by Normalize.

Usage

NormalizeMPX(
  object,
  method = c("dsb", "clr"),
  isotype_controls = c("mIgG1", "mIgG2a", "mIgG2b"),
  assay = NULL,
  ...
)

# S3 method for class 'Matrix'
NormalizeMPX(
  object,
  method = c("dsb", "clr"),
  isotype_controls = c("mIgG1", "mIgG2a", "mIgG2b"),
  ...
)

# S3 method for class 'MPXAssay'
NormalizeMPX(
  object,
  method = c("dsb", "clr"),
  isotype_controls = c("mIgG1", "mIgG2a", "mIgG2b"),
  ...
)

# S3 method for class 'Assay'
NormalizeMPX(
  object,
  method = c("dsb", "clr"),
  isotype_controls = c("mIgG1", "mIgG2a", "mIgG2b"),
  ...
)

# S3 method for class 'CellGraphAssay'
NormalizeMPX(
  object,
  method = c("dsb", "clr"),
  isotype_controls = c("mIgG1", "mIgG2a", "mIgG2b"),
  ...
)

# S3 method for class 'Assay5'
NormalizeMPX(
  object,
  method = c("dsb", "clr"),
  isotype_controls = c("mIgG1", "mIgG2a", "mIgG2b"),
  ...
)

# S3 method for class 'CellGraphAssay5'
NormalizeMPX(
  object,
  method = c("dsb", "clr"),
  isotype_controls = c("mIgG1", "mIgG2a", "mIgG2b"),
  ...
)

# S3 method for class 'PNAAssay'
NormalizeMPX(
  object,
  method = c("dsb", "clr"),
  isotype_controls = c("mIgG1", "mIgG2a", "mIgG2b"),
  ...
)

# S3 method for class 'PNAAssay5'
NormalizeMPX(
  object,
  method = c("dsb", "clr"),
  isotype_controls = c("mIgG1", "mIgG2a", "mIgG2b"),
  ...
)

# S3 method for class 'Seurat'
NormalizeMPX(
  object,
  method = c("dsb", "clr"),
  isotype_controls = c("mIgG1", "mIgG2a", "mIgG2b"),
  assay = NULL,
  ...
)

Arguments

object: An object.
method: The normalization method to use. Can be "dsb" or "clr".
isotype_controls: A vector of isotype controls to use for normalization.
assay: Name of assay to use; defaults to the default assay.
...: Additional arguments. Currently not used.

Value

An object with normalized MPX data.