mx_normalize {mxnorm}

Normalizes multiplexed data

Description

Normalizes some given image input according to the method specified

Usage

mx_normalize(
  mx_data,
  transform = "None",
  method = "None",
  method_override = NULL,
  method_override_name = NULL,
  ...
)

Arguments

mx_data

mx_dataset object to normalize

transform

transformation to perform on the input data. Options include: c("None", "log10", "mean_divide","log10_mean_divide")

method

normalization method to perform on the input data. Options include: c("None", "ComBat","Registration")

method_override

optional user-defined function to perform own normalization method (default=NULL). If using a user-defined function, it must include a mx_data parameter.

method_override_name

optional name for method_override (default=NULL).

...

optional additional arguments for normalization functions

Value

Multiplexed data normalized according to the method specified, in the mx_dataset format. Normalized data will be included a new table with normalized values and attributes describing the transformation.

Examples

mx_data = mx_dataset(mxnorm::mx_sample, "slide_id", "image_id",
  c("marker1_vals","marker2_vals","marker3_vals"),
  c("metadata1_vals"))
mx_data = mx_normalize(mx_data, transform="log10",method="None")