nsSNPCalculatebyRange: Calculates percentage of nsSNPs by gene range

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

Description

A function that integrate the information from bioMart and calculates the percentage of positions could involve nsSNP of protein encoding range in given chromosome, gene range (start coordinate, end coordinate).

Usage

nsSNPCalculatebyRange(chrName, startPosition, endPosition)

Arguments

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.

Value

Returns a data frame object including the query and evaluated results

• geneName - A value of class "character" indicating the gene name

• lengths - A value of integer indicating the transcript length

• nsSNPs - A value of class "numeric" indicating the nsSNP-involved locations over the transcript

• percent - A value of class "numeric" indicating the percentage of nsSNP over the transcript

References

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.

Examples

# 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

# Calculates percentage of nsSNPs in chromosome 3 gene range 49359145 to 49411645
nsSNPCalculatebyRange(chrName = 3,
                     startPosition = 49359145,
                     endPosition = 49411645)

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