nameB: names latent variables according to their pathway useage (if...

In wgmao/PLIER: Pathway-Level Information Extractor (PLIER): a generative model for gene expression data

names latent variables according to their pathway useage (if any)

Description

names latent variables according to their pathway useage (if any)

Usage

nameB(plierRes, top = 1, fdr.cutoff = 0.01, use = c("coef", "AUC"))

Arguments

plierRes	A PLIER result
top	The number of pathway to use. Only the top pathway (one with the largest coefficient) is used by default
fdr.cutoff	The cross-validation significance cutoff for a pathway to be considered for naming. If no pathways satisfy the cutoff the raw coefficients are used.
Choice	of coef or AUC, whether LVs are named based on U coefficients or AUCs. Defualt: coef.

wgmao/PLIER documentation built on May 11, 2022, 10:34 p.m.