autoPLIER.get_top_pathway_LVs: AutoPLIER Get Top Pathways LVs Method

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

AutoPLIER Get Top Pathways LVs Method

Description

Retrieve LVs associated with a named pathway.

Usage

autoPLIER.get_top_pathway_LVs(ap, ...)

Arguments

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

Details

Additional arguments

• pathway - List of pathways.

• n_LVs - Number of latent variables to retrieve.

Value

Numeric object with the chosen pathway and its corresponding LVs.

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 and transform
mod <- autoPLIER(n_components = 50)
autoPLIER.fit_transform(mod, x_train = xtrain, pathways = pwy, maxepoch=100L, verbose=0)

# Get LVs for a pathway
mod <- autoPLIER.get_top_pathway_LVs(mod, pathway="BIOCARTA_VDR_PATHWAY", n_LVs=2L)

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