README.md

In Jiyun1201/CANMutVisual: Analyze and Visualize Cancer Mutation Data

CANMutVisual

Description

The goal of CANMutVisual is to allow simple visualization of large tsv cancer gene data file. With continuous addition of cancer gene data, it is difficult to communicate and transfer knowledge on cancer genome analysis. Therefore, CANMutVisual tool provide a path to expand on simplification of cancer genome research by visualizaing the data. The package take in data files and process it to simplify and extract necessary data to produce organized data frame. This package also provides functions to plot the extracted data to visualize the genomic mutational frequency in specific type of cancer. The package is intended for BCB410H bioinformatics R package development.

Installation

To install the latest version of CANMutVisual pacakge:

require("devtools")
devtools::install_github("Jiyun1201/CANMutVisual", build_vignettes = TRUE)
library("CANMutVisual")

To run the shinyApp:

CANMutVisual::runCANMutVisual()

Overview

ls("package:CANMutVisual")
data(package = "CANMutVisual") # optional

CANMutVisual contains 5 functions for users:

1. cosImport function reads .tsv file that contain specific cancer types' gene data (which will be inputed from users) and common approved HGNC id file (which is already provided in the Data folder). Then, the function extracts only the necessary columns of data and return the resulting data frame.

2. countMut function uses cosImport function in cosImport.R file to read from cosmic file and uses that dataframe to extract IDsymbol column and return the occurrence frequency of each gene types.

3. mut_cds function uses cosImport function in cosImport.R file to read from cosmic file and uses that dataframe to obtain MUTATION_CDS column The last three letters are extracted and compared with mutValue list and unmatched elements are deleted. Then, dataframe with two columns returned.

4. plot_top_15 function uses countMut function in countMut.R file to get frequency data of each gene and return piechart using the data extracted.

5. plot_cds function uses mut_cds function in mut_cds.R file to get frequency data of each mutation and return barplot using the data extracted

Refer to vignette for more details:

browseVignettes(package = "CANMutVisual")

An overview of the package is illustrated below:

.
├── CANMutVisual.Rproj
├── DESCRIPTION
├── LICENSE
├── NAMESPACE
├── README.md
├── Data
│   ├── HGNC.tsv
│   └── MutantData.tsv
├── R
│   ├── cosImport.R
│   ├── gcountMut.R
│   ├── gene_mut_plot.R
│   ├── mut_cds.R
│   └── plot_cds.R
├── man
│   │
│   └── hello.Rd
├── inst
│   └── extdata
│       └── CANMutVisual.png
├── tests
│   ├── testthat
│   │   ├── test_cosImport.R
│   │   ├── test_countMut.R
│   │   ├── test_gene_mut_plot.R
│   │   ├── test_mut_cds.R
│   │   └── test_plot_cds.R
│   └── testthat.R
└── vignettes
    ├── plot_top_15_result.png
    ├── cosImport_result.png
    ├── countMut_result.png
    ├── mut_cds_result.png
    ├── cosImport_result.png
    └── plot_cds_result.png

Contributions

The author of this package is Jiyun Won.

The readr package is used for cosImport function to read cosmic .tsv files. The plotrix package is used to plot 3D pie graph in plot_top_15 function. The str_sub in stringr package is used to extract last three letters of character elements in mut_cds function.

References

Cosmic. (2021, May 28). Data downloads (release V94, 28th May 2021). Download Files. Retrieved November 21, 2021, from https://cancer.sanger.ac.uk/cosmic/download.

Custom downloads HGNC. HGNC. (n.d.). Retrieved November 21, 2021, from https://www.genenames.org/download/custom/.

Wickham, H., Hester, J., & Francois, R. (2021, November 11). Read rectangular text data [R package readr version 2.1.0]. The Comprehensive R Archive Network. Retrieved November 21, 2021, from https://cran.r-project.org/web/packages/readr/index.html.

Wickham, H. (n.d.). stringr: Simple, Consistent Wrappers for Common String Operations. Introduction to stringr. Retrieved November 21, 2021, from https://cran.r-project.org/web/packages/stringr/vignettes/stringr.html.

Lemon, J., Bolker, B., Oom, S., & Klein, E. (n.d.). Package plotrix. CRAN. Retrieved November 22, 2021, from https://cran.r-project.org/web/packages/ plotrix/index.html.

Kabacoff , R. (n.d.). Bar plots. Quick-R: Bar Plots. Retrieved November 21, 2021, from https://www.statmethods.net/graphs/bar.html.

Abedin, J., & Mittal, H. V. (n.d.). R Graphs. R Graphs Cookbook (Second Edition) - Displaying values on top of or next to the bars. Retrieved November 21, 2021, from https://subscription.packtpub.com/book/big_data_and_business_ intelligence/9781783988785/6/ch06lvl1sec69/displaying-values-on-top-of-or- next-to-the-bars.

Acknowledgements

This package was developed as part of an assessment for 2021 BCB410H: Applied Bioinformatics, University of Toronto, Toronto, CANADA.

Jiyun1201/CANMutVisual documentation built on Dec. 18, 2021, 1:38 a.m.