autoPLIER.transform: AutoPLIER Transform Method

In Bishop-Laboratory/autoplieR: What the Package Does (One Line, Title Case)

AutoPLIER Transform Method

Description

Applies the fitted calculation to the created autoPLIER model.

Usage

autoPLIER.transform(ap, ...)

Arguments

ap	AutoPLIER object.
...	Additional arguments for autoPLIER.transform. See details.

Details

Additional arguments

• x_predict - Dataset to be transformed into the latent space.

• pathways - Pathways dataset.

Value

A dataframe consisting of a number of LV columns as specified by the n_components in autoPLIER().

Examples

# Example datasets
xtrain <- read.csv(system.file("extdata", "GSE157103_icu_tpm.csv.xz", package = "autoplieR"),
 row.names = 1)
pwy <- read.csv(system.file("extdata", "pathways.csv.xz", package = "autoplieR"),
 row.names = 1)

# Fit the model
mod <- autoPLIER(n_components = 50)
mod <- autoPLIER.fit(mod, x_train = xtrain, pathways = pwy, maxepoch=100L, verbose = 0)

# Transform
df_ap <- autoPLIER.transform(mod, x_predict = xtrain, pathways = pwy)

Bishop-Laboratory/autoplieR documentation built on July 11, 2022, 4:49 a.m.