README.md

In Yuewei-Wang/nsSNPfinder: nsSNP Postion Finder and Visualization

nsSNPfinder

Description

nsSNPfinder is an R package for integrating, analyzing, and visualizing the SNP data from the genomic level to the protein level, finding potential nsSNP-associated gene marker that might cause the protein structure change. This package was developed using R version 4.1.1 and x86_64-apple-darwin17.0 (64-bit) platform runnning under macOS Monterey 12.0.1.

Installation

You can install the development version of nsSNPfinder from GitHub with:

# install.packages("devtools")
require("devtools")
devtools::install_github("Yuewei-Wang/nsSNPfinder", build_vignettes = TRUE)
library(nsSNPfinder)

To run the shinyApp:

runNSSNPfinder()

Overview

ls("package:nsSNPfinder")

nsSNPfinder contains 4 functions to demonstrate the nsSNP distribution in certain H. sapiens gene and address the protein structure of the gene.

The nsSNPCalculatebyRange function calculates the percentage of residues involving nsSNP event in the gene region.

The SNPFreqPlot function generates the plot to indicate the position distribution of SNPs within the certain gene region.

The nsSNPFreqPlot function generates the plot similar as SNPFreqPlot but the targets are all nsSNPs within the gene.

The displayPDB function displays the encoded-protein 3D structure record in PBD or UniProt, and highlight the residue positions involved nsSNPs.

browseVignettes("nsSNPfinder")

Contributions

The author of the package is Yuewei Wang. The nsSNPCalculatebyRange function utilized the SNPlocs.Hsapiens.dbSNP144.GRCh38 and BSgenome.Hsapiens.UCSC.hg38 to obtain the initial information of SNP locations and human chromosome sequences. The biomaRt package is used for collecting the genomic sequences and type of variants. GENETIC_CODE function in Biostrings package is used for compare the codon, which contributes to find potential nsSNPs.

The nsSNPFreqPlot and SNPFreqPlot functions use map function from ggplot2 R package to generate frequency plots.

The displayPDB function use the function from prort and model visualization function from r3dmol R packages to obtain the Uniprot recorded protein sequence and pdb file of structure modelling..

Reference

Durinck, S., Spellman, P., Birney, E.,& Huber, W. (2009). Mapping identifiers for the integration ofgenomic datasets with the R/Bioconductor package biomaRt. Nature Protocols, 4, 1184–1191.2.

Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., De Moor, B., Brazma, A.,& Huber, W. (2005).BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.Bioinformatics, 21, 3439–3440.

Pagès, H., Aboyoun, P., Gentleman, R., DebRoy, S. (2021). Biostrings: Efficient manipulation of biological strings. R package version 2.62.0.

Pagès, H. (2017). SNPlocs.Hsapiens.dbSNP144.GRCh38: SNP locations for Homo sapiens (dbSNPBuild 144). R package version 0.99.20.

Pagès, H. (2021). BSgenome: Software infrastructure for efficient representation of full genomes and their SNPs. R package version 1.62.0.

Su, W (2020). r3dmol: Create Interactive 3D Visualizations of Molecular Data. R package version 0.1.0. https://github.com/swsoyee/r3dmol

Team TBD (2021). BSgenome.Hsapiens.UCSC.hg38: Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p13). R package version 1.4.4.

Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org.

Xiao, N., Cao, DS., Zhu, MF., Xu, QS. (2015). protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences. Bioinformatics 31 (11), 1857-1859.

Acknowledgements:

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

Q&A

• How to solve the timeout error in installation:

Due to the size of data packages (BSgenome.Hsapiens.UCSC.hg38 and SNPlocs.Hsapiens.dbSNP144.GRCh38), sometimes the timeout error occurs in the process of installing packages. You can increase the timeout setting by:

library("utils")
# set to 300s (5mins)
options(timeout = 300)

to solve the error. Then running installation would work.

Yuewei-Wang/nsSNPfinder documentation built on Dec. 18, 2021, 8:21 p.m.