autoPLIER.get_top_pathways: AutoPLIER Get Top Pathways Method

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

AutoPLIER Get Top Pathways Method

Description

Retrieve pathways most related to a list of LVs with coefficients.

Usage

autoPLIER.get_top_pathways(ap, LVs, n_pathways)

Arguments

ap	AutoPLIER object.
LVs	List of decomposed latent variables in an array.
n_pathways	Number of pathways to retrieve.

Value

A list containing sub-lists for each listed LV.

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 top pathways
autoPLIER.get_top_pathways(mod, array(c("LV_38", "LV_30")), n_pathways = 2)

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