transform: Transform/normalize expression data
In igordot/phenomenalist: Analysis Toolkit for PhenoCycler (CODEX) Data in R
transform R Documentation
Transform/normalize expression data
Description
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.
igordot/phenomenalist documentation built on March 1, 2024, 1:41 p.m.
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| transform | R Documentation |
Transform/normalize expression data
Description
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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