Feature screening for survival trait with application to TCGA high-dimensional genomic data

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Bioinformatics and Genomics

Main article text

 

Introduction

Materials and Methods

Data structure and methods partial review

TCGA cancer data source

Evaluation performance in the simulation study

Simulation scenarios

so the underlying survival model has 14 true predictors. In the first simulated settings, only linear relationships were assumed with true parameter vector. The censoring time distribution follows a uniform distribution U(a,b), where (a,b) is chosen to control the censoring rate at about 30% (light censoring), 50% (middle censoring) and 70% (heavy censoring) respectively. Moreover, we consider the setting where, with a probability of 0.1, the covariates may be contaminated by outliers produced by a t distribution with two degrees of freedom.

Survival prediction measure in real data application

Results

Simulation studies

Real data application with TCGA ESCA data

Real data application with TCGA PAAD data

Conclusions and disscussions

Supplemental Information

Supplemental Figures and Tables.

DOI: 10.7717/peerj.13098/supp-1

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Jie-Huei Wang conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Cai-Rong Li performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Po-Lin Hou performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

R codes for the simulation studies and real data are available at Figshare: Wang, Jie-Huei (2021): The R code for the paper entitled “Feature Screening for Survival Trait with Application to TCGA High-dimensional Genomic Data”. figshare. Software. https://doi.org/10.6084/m9.figshare.16677070.v3.

The TCGA ESCA, PAAD, LUAD, and BRCA genomic data with survival traits analyzed during this study are all available at Figshare: Wang, Jie-Huei (2021): The TCGA cancer data for the paper entitled “Feature Screening for Survival Trait with Application to TCGA High-dimensional Genomic Data”. figshare. Dataset. https://doi.org/10.6084/m9.figshare.16677619.v2.

Funding

This work was supported by the grant MOST 110-2118-M-035-001-MY2 from the Ministry of Science and Technology of Republic of China (Taiwan). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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