snpGeneSets

snpGeneSets annotates and analyzes genome-wide study (GWS) results by mapping single nucleotide polymorphisms (SNPs) to genes and gene sets, estimating gene-level effects from SNP associations, and performing gene set enrichment analyses to interpret SNPs, gene expression, and gene-set associations.

Key Features:

• Integration of local knowledge bases: Incorporates local copies of comprehensive databases for SNPs, genes, and gene sets to support annotation and mapping.
• R wrapper functions: Exposes wrapper functions in R to access low-level databases and programmatically perform annotation tasks.
• Support for next-generation sequencing GWS results: Targets annotation and analysis of genome-wide study outputs generated from next-generation sequencing technologies.
• Genomic mapping and functional annotation: Provides genomic mapping annotations for SNPs and genes and functional annotations for gene sets.
• Bidirectional mapping: Supports mapping from SNPs to genes and from genes to gene sets, and the reverse directions.
• Gene effect measures and enrichment analyses: Calculates gene effect measures from SNP associations and performs gene set enrichment analyses.

Scientific Applications:

• Annotation and enrichment of GWS results: Annotates genome-wide study results and performs enrichment analyses to identify functional pathways and biological implications.
• Type 2 diabetes (T2D) GWAS (NHGRI GWAS catalog): Applied to T2D results from the NHGRI GWAS catalog for annotation and pathway-level interpretation.
• Finnish GWAS: Applied to a Finnish genome-wide association study for SNP-to-gene and gene-set annotation.
• Genome-wide expression study (GWES): Applied to GWES data to relate gene expression signals to SNPs and gene sets.

Methodology:

Leverages local knowledge bases and R-based wrapper functions to access low-level databases, performs genomic mapping annotations for SNPs and genes, supports bidirectional SNP↔gene and gene↔gene-set mapping, calculates gene effect measures from SNP associations, and executes gene set enrichment analyses.