SubtypeSpecificGene: GeneCluster: Identification of subtype-specific genes

In huynguyen250896/GeneCluster: GeneCluster: Identification of subtype-specific genes

Description

A previous study defined subtype-specific genes are the ones mutated predominantly in the samples assigned to one single subtype than in the other subtypes. Subsequently, those genes are genomic features that reflect the difference between subgroups of heterogeneous cancers. To computationally detect subtype-specific genes, we built the R package GeneCluster from the idea of the reference paper. In brief, given a gene from a list of genes of interest, it will be specifically distributed to either of predictive subgroups based on the mean values (e.g., CNA changes, MET changes, and expression levels). Then, a gene was considered as a subtype-specific one if P-value <= 0.05 (one-way ANOVA test). For further information on requirements as well as how to implement this tool, please visit my Github repository: https://github.com/huynguyen250896/GeneCluster

Usage

SubtypeSpecificGene(omics, cluster, adjustedP = T)

Arguments

omics	data.frame or matrix. omics includes its rows are samples and its columns are genomic features.
cluster	numeric. Predictive subgroups correspond with samples after running a clustering tool for your own data (e.g., k-means, hclust,...).
adjustedP	logical. Whether we should adjust the gained P-values (one-way ANOVA test) using the Benjamini-Hochberg procedure. Default is adjustedP = T

Author(s)

Quang-Huy Nguyen

References

Quang-Huy Nguyen, Duc-Hau Le. (2020). Multi-omics analysis detects novel prognostic subgroups of breast cancer. Frontiers in Genetics, 11(1265).

Examples

SubtypeSpecificGene(omics = exp, cluster = groups)

huynguyen250896/GeneCluster documentation built on Feb. 20, 2021, 1:23 a.m.