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Transform/normalize expression data

Source: R/transform.R
transform.Rd

Transform/normalize expression data. The options are currently:

  • log: log10 + 1

  • z: Z normalization of each marker (recommended by Hickey et al.)

Usage

transform(x, method = c("log", "z"), out_dir = NULL)

Arguments

x

A SpatialExperiment object.

method

A character string indicating which transformation method should be used.

out_dir

Name of the output directory. If specified, the density plots will be saved there.

Value

A SpatialExperiment object with transformed values in the exprs assay.