SNPFreqPlot: Generate a plot of SNP locations versus number of nucleotide...
In Yuewei-Wang/nsSNPfinder: nsSNP Postion Finder and Visualization

Description Usage Arguments Value References Examples

View source: R/SNPFreqPlot.R

A function that integrate the information from bioMart and plot the SNP positions over the protein encoding range in given chromosome, gene range (start coordinate, end coordinate). For better resolution, the genome range is limited within 200-nt length.

1	SNPFreqPlot(chrName, startPosition, endPosition)

`chrName`	A integer value of class "numeric" indicating the human chromosome 1-22, or a char either in 'X' or 'Y' indicating human sex chromosome.
`startPosition`	A positive integer indicating the starting coordinate of gene range.
`endPosition`	A positive integer indicating the end coordinate of gene range.

Returns a plot indicating the overview situation of SNPs

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, https://bioconductor.org/packages/Biostrings.

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

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

# The used dataset of SNPs is default from SNPlocs.Hsapiens.dbSNP144.GRCh38 package
# The used dataset of Human genome is default from BSgenome.Hsapiens.UCSC.hg38 package

# Generate the SNP locations in chromosome 3 in region of 49395438 to 49395450
SNPFreqPlot(chrName = 3,
           startPosition = 49395520,
           endPosition = 49395566)