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. pathwayPCA is an open-source R package, freely available through the Bioconductor repository. pathwayPCA is expected to be a useful tool for empowering the wider scientific community to analyze and interpret the wealth of available proteomics data, along with other types of molecular data recently made available by Clinical Proteomic Tumor Analysis Consortium and other large consortiums.

journal_name

Proteomics

journal_title

Proteomics

authors

Odom GJ,Ban Y,Colaprico A,Liu L,Silva TC,Sun X,Pico AR,Zhang B,Wang L,Chen X

doi

10.1002/pmic.201900409

subject

Has Abstract

pub_date

2020-11-01 00:00:00

pages

e1900409

issue

21-22

eissn

1615-9853

issn

1615-9861

journal_volume

20

pub_type

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