PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data.

ABSTRACT: The authors present pathwayPCA, an R/Bioconductor package for integrative pathway analysis that utilizes modern statistical methodology, including supervised and adaptive, elastic-net, sparse principal component analysis. pathwayPCA can be applied to continuous, binary, and survival outcomes in studies with multiple covariates and/or interaction effects. It outperforms several alternative methods at identifying disease-associated pathways in integrative analysis using both simulated and real datasets. In addition, several case studies are provided to illustrate pathwayPCA analysis with gene selection, estimating, and visualizing sample-specific pathway activities, identifying sex-specific pathway effects in kidney cancer, and building integrative models for predicting patient prognosis. pa

SUBMITTER: Odom GJ 

PROVIDER: S-EPMC7677175 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature