GitHub - rongxinzh/G4SNVHunter (original) (raw)

G4SNVHunter

G4SNVHunter is an R package leveraging the G4Hunter algorithm to systematically identify single nucleotide variants (SNVs), along with other small-scale variants such as indels and MNVs, that have the potential to disrupt G-quadruplex (G4) formation propensity.

Installation

Option 1: Install from GitHub

You can install the package directly from GitHub,

install.packages("devtools")

devtools::install_github("rongxinzh/G4SNVHunter")

To run the sample code in our vignette, set the dependencies parameter to TRUE,

install.packages("devtools")

devtools::install_github("rongxinzh/G4SNVHunter", dependencies = TRUE)

NOTE

• Your R version must be ≥ 4.3.
• If you are using Windows, please installRtoolsbefore proceeding.

Option 2: Install from Bioconductor

The package is also available on Bioconductor as a development (devel) version. To install it, follow these steps,

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, set dependencies to TRUE,

BiocManager::install("G4SNVHunter", dependencies = TRUE)

NOTE

• The Bioconductor installation (version = 'devel') requires the latest version of R.
• Make sure to initialize Bioconductor devel usingBiocManager::install(version = 'devel') before installing the package.

Quick Start

First, you need to library the G4SNVHunter package,

In this example, we need to use the human genome sequence of chromosome 16 (hg19 version).

if (!requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)) { BiocManager::install("BSgenome.Hsapiens.UCSC.hg19") } library(BSgenome.Hsapiens.UCSC.hg19)

Load sequence for chromosome 16 (hg19)

hg19 <- BSgenome.Hsapiens.UCSC.hg19

chr16_seq <- DNAStringSet(hg19$chr16)

Chromosome names are needed for analysis

names(chr16_seq) <- "chr16"

We have prepared some sample variant data, which can be loaded as,

vcf_file <- system.file("extdata", "example_variants_chr16.vcf", package = "G4SNVHunter") variants <- loadVariant(vcf_file, file_type = "vcf") seqlevels(variants) <- paste0("chr", seqlevels(variants))

Before assessing the impact of SNV on G4, we need to predict the G4-prone regions,

chr16_G4 <- G4HunterDetect(chr16_seq)

Then, the impact of variants on the formation of G4 structures can be evaluated as,

result <- G4VarImpact(G4 = chr16_G4, variants = variants, ref_col = "REF", alt_col = "ALT")

Since not all variants 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:

filtered_var_eff <- filterVarImpact(result, raw_score_threshold = 1.5, mut_score_threshold = 1.2)

print(filtered_var_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(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.

Contact

For additional inquiries, contact us at: Email: rongxinzhang@outlook.com