# G4SNVHunter <img src="./vignettes/images/logo.png" align = "right" width = "150" />
G4SNVHunter is an R package leveraging the G4Hunter algorithm to systematically
identify single nucleotide variants (SNVs), including single nucleotide
polymorphisms (SNPs), with the potential to disrupt the formation of
G-quadruplex (G4) structures.
# Installation
### Option 1: Install from GitHub
You can install the package directly from GitHub,
```r
# install.packages("devtools")
devtools::install_github("rongxinzh/G4SNVHunter")
```
To run the sample code in our [vignette](
https://bioconductor.org/packages/devel/bioc/vignettes/G4SNVHunter/inst/doc/G4SNVHunter.html
), set the `dependencies` parameter to `TRUE`,
```r
# install.packages("devtools")
devtools::install_github("rongxinzh/G4SNVHunter", dependencies = TRUE)
```
**NOTE**
* Your R version must be ≥ 4.3.
* If you are using Windows, please install
[Rtools](https://ohdsi.github.io/Hades/rSetup.html#Installing_RTools)
before proceeding.
### Option 2: Install from Bioconductor
The package is also available on Bioconductor as a development (devel) version.
To install it, follow these steps,
```r
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = 'devel')
BiocManager::install("G4SNVHunter")
```
If you want to run the sample code in our [vignette](
https://bioconductor.org/packages/devel/bioc/vignettes/G4SNVHunter/inst/doc/G4SNVHunter.html
),
set `dependencies` to `TRUE`,
```r
BiocManager::install("G4SNVHunter", dependencies = TRUE)
```
**NOTE**
* The Bioconductor installation (`version = 'devel'`) requires the latest
version of R.
* Make sure to initialize Bioconductor devel using
`BiocManager::install(version = 'devel')` before installing the package.
# Quick Start
First, you need to library the G4SNVHunter package,
```r
library(G4SNVHunter)
```
In this example, we need to use the human genome sequence of chromosome 21
(hg19 version).
```r
if (!requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)) {
BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
}
library(BSgenome.Hsapiens.UCSC.hg19)
# Load sequence for chromosome 21 (hg19)
hg19 <- BSgenome.Hsapiens.UCSC.hg19
chr21_seq <- DNAStringSet(hg19$chr21)
# Chromosome names are needed for analysis
names(chr21_seq) <- "chr21"
```
We have prepared some sample variant data, which can be loaded as,
```r
data(snv_gr)
```
Before assessing the impact of SNV on G4, we need to predict the G4-prone
regions,
```r
chr21_G4 <- G4HunterDetect(chr21_seq)
```
Then, the impact of SNVs on the formation of G4 structures can be evaluated as,
```r
snv_eff <- SNVImpactG4(chr21_G4, snv_gr, alt_col = "alt")
```
Since not all SNVs can significantly impact the formation of G4s, we need to
filter the output. While the filtering parameters can be set flexibly, a set of
recommended parameters is:
```r
filtered_snv_eff <- filterSNVImpact(snv_eff,
raw_score_threshold = 1.5,
mut_score_threshold = 1.2)
print(filtered_snv_eff)
```
Generally, G4 structures with an absolute G4Hunter score above 1.5 are
considered to have a high confidence in forming stable structures. In contrast,
those with scores below 1.2, or more conservatively, below 1.0, are typically
less likely to form stable structures.
# Vignette
For full use of our package, please refer to our [vignette](
https://bioconductor.org/packages/devel/bioc/vignettes/G4SNVHunter/inst/doc/G4SNVHunter.html)
(highly recommended).
# Bug Reports
If you encounter any issues, have questions, or would like to make suggestions,
feel free to report them at our [bug tracker](
https://github.com/rongxinzh/G4SNVHunter/issues).
# Contact
For additional inquiries, contact us at:
Email: rongxinzhang@outlook.com
