README.md

In huynguyen250896/DrGA: DrGA: driver gene analysis in an automatic manner

DrGA: cancer driver gene analysis in a simpler manner

I. Introduction

DrGA is a novel R package that has been developed based on the idea of our most recent driver gene analysis scheme here. It wholly automates the analysis process and attached improvements to maximize user experience with the highest convenience. In particular, it facilitates users with limited IT backgrounds and rapidly creates consistent and reproducible results. We describe the usage of the DrGA on driver genes of human breast cancer using a multi-omics dataset. Besides, we also provide users with another potential application of DrGA on analyzing genomic biomarkers of a complex disease from other species.

II. Understanding the tool and Data Structure

The following are parameters included in DrGA and their role: - organism: organism name. Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - hsapiens, mouse - mmusculus. Default is organism = "hsapiens".

• sources: possible biological mechanisms allowed (e.g., Gene Ontology - GO:BP, GO:MF, GO:CC; KEGG; REAC; TF; MIRNA; CORUM; HP; HPA; WP;… Please see the g:GOSt web tool for the comprehensive list and details on incorporated data sources). Default is sources = c("GO:BP", "KEGG").

• methodCC: Correlation method type. Allowed values are spearman (default), pearson, kendall.

• exp: a data frame or matrix. exp has its rows are samples and its columns are genes. It is input data to serve to run the second and third modules.

• clinicalEXP: a data frame or matrix. It includes its rows are samples, and its columns are clinical features of your choice. Note that if users want to perform survival analysis, clinicalEXP must have two columns as overall survival time (continuous variable) and overall survival status (binary variable; usually coded 1 as death and 0 as live) of all the subjects.

• timeEXP: a vector of overall survival time. It is a column vector of clinicalEXP.

• statusEXP: a vector of overall survival time. It is a column vector of clinicalEXP.

• datMODULE4: a data frame or matrix. datMODULE4 has its rows are samples and its columns are genes. It is input data to serve to run the forth module.

• cliMODULE4: a data frame or matrix. It includes its rows are samples, and its columns are clinical features of your choice. Note that if users want to perform survival analysis, cliMODULE4 must have two columns as overall survival time (continuous variable) and overall survival status (binary variable; usually coded 1 as death and 0 as live) of all the subjects.

• timeMODULE4: a vector of overall survival time. It is a column vector of cliMODULE4.

• statusMODULE4: a vector of overall survival time. It is a column vector of cliMODULE4.

• minClusterSize: Minimum cluster size. minClusterSize = 10 is default.

• NetworkType: network type. Allowed values are (unique abbreviations of) unsigned, signed, signed hybrid. Default value is signed.

• hm_row_names: logical. If hm_row_names = TRUE (default value), gene names appear in rows of the heatmap. If due to the large number of driver genes leading to impossibly showing gene names in rows of the heatmap, users can turn them off by hm_row_names = FALSE.

Please download datasets data_n_code and read Supplementary Materials (highly recommended) as examples to well grasp DrGA's easy-to-meet format and its usage.

III. Pipeline

Figure: Pipeline of the package DrGA.

IV. Implementation

Use the following command to install directly from GitHub;

devtools::install_github("huynguyen250896/DrGA", dependencies = T)

Call the nescessary libraries;

x = c("DrGA", "dplyr", "survival", "tibble", "tidyr", "ComplexHeatmap", 
     'cluster', 'mclust', 'clValid', 'Biobase', 'annotate', 'GO.db', 
     'mygene', "dynamicTreeCut", "flashClust", "Hmisc", "WGCNA","purrr",
     "gprofiler2", "table1", "compareGroups")
lapply(x, require, character.only = TRUE)

running example:

drga = DriverGeneAnalysis(exp = exp, clinicalEXP = clinicalEXP, timeEXP = clinicalEXP$time, statusEXP = clinicalEXP$status, 
                   datMODULE4 = cna,  cliMODULE4 = clinicalCNA, timeMODULE4 = clinicalCNA$time, statusMODULE4 = clinicalCNA$status)

V. Citation

Please kindly cite the following paper (and Star this Github repository if you find this tool of interest) if you use the tool in this repo:

Reference Type: Journal Article
Author: Nguyen, Quang-Huy
Nguyen, Tin
Le, Duc-Hau
Year: 2022
Title: DrGA: cancer driver gene analysis in a simpler manner
Journal: BMC Genomics
Volume: 23
Issue: 1
Pages: 86
Date: 2022/03/05
ISSN: 1471-2105
DOI: 10.1186/s12859-022-04606-0

Feel free to contact Quang-Huy Nguyen for any questions about the code and results.

huynguyen250896/DrGA documentation built on Oct. 18, 2023, 5:47 a.m.