https://github.com/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"
https://github.com/javadr/r-test
biomedical-data-science
Last synced: 3 months ago
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The solutions to two biomedical problems including finding "the list of differentially expressed genes" and "the 3 most frequently mutated genes in liver cancer"
- Host: GitHub
- URL: https://github.com/javadr/r-test
- Owner: javadr
- License: agpl-3.0
- Created: 2021-08-15T12:14:38.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2022-03-30T17:14:40.000Z (about 3 years ago)
- Last Synced: 2025-01-14T16:28:40.259Z (5 months ago)
- Topics: biomedical-data-science
- Language: TeX
- Homepage:
- Size: 841 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: Readme.md
- License: LICENSE
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README
# 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](https://www.uthscsa.edu/academics/biomedical-sciences/faculty/profile/65296/Zare,-Habil) at [OncInfo lab](https://www.oncinfo.org/r_test).
# 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](https://www.oncinfo.org/r_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.**