Bioinformatics. 2023 Dec 7:btad741. doi: 10.1093/bioinformatics/btad741. Online ahead of print.
ABSTRACT
SUMMARY: Densely measured SNP data is routinely analyzed but faces challenges due to its high dimensionality, especially when gene-environment (G-E) interactions are incorporated. In recent literature, a functional analysis strategy has been developed, which treats dense SNP measurements as a realization of a genetic function and can “bypass” the dimensionality challenge. However, there is a lack of portable and friendly software, which hinders practical utilization of these functional methods. We fill this knowledge gap and develop the R package FunctanSNP. This comprehensive package encompasses estimation, identification, and visualization tools and has undergone extensive testing using both simulated and real data, confirming its reliability. FunctanSNP can serve as a convenient and reliable tool for analyzing SNP and other densely measured data.
AVAILABILITY: The package is available at https://CRAN.R-project.org/package=FunctanSNP.
SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.
PMID:38060266 | DOI:10.1093/bioinformatics/btad741
