javadr/R-Test

The solutions to two biomedical problems including finding "the list of differentially expressed genes" and "the 3 most frequently mutated genes in liver cancer"

R-Test

The solutions to two biomedical problems including finding "the list of differentially expressed genes" and "the 3 most frequently mutated genes in liver cancer" with the aid of R language.

This repository solves the problems defined by Professor Habil Zare at OncInfo lab.

Installing dependencies

To run the scripts the following packages should be installed:

tictoc, pheatmap, calibrate, dplyr, DT
TCGAbiolinks, GEOquery, maftools, limma

To install these libraries, you would proceed as:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("GEOquery", "TCGAbiolinks", "maftools", "limma"))

install.packages(c("tictoc", "pheatmap", "calibrate", "DT"))	

Solutions

1. Question 2 [differentially expressed genes]: Computes the list of differentially expressed genes with adjusted p-value better than 0.01 for GSE59259 dataset. It also uses pheatmap function to plot the expression of the top 5 DE genes.

2. Question 3 [mutated genes in liver cancer]: It determines the 3 most frequently mutated genes in liver cancer using the maftools and TCGAbiolinks packages. The solution also applies KM plot to find out which of these 3 mutations is more predictive of survival.

3. Miscellaneous [Gauss-Jordan algorithm]: There is another file in this repository which implements Gauss-Jordan algorithm in solving system of linear equations, named ssle.R

Warning

If you are using these codes or getting some ideas from them for the above-mentioned test, it's mandatory to put this repository in your references as well as informing Professor Zare. Remember that he knows well about this repository.