SnpGeneSets: An R Package for Genome-Wide Study Annotation.

ABSTRACT: Genome-wide studies (GWS) of SNP associations and differential gene expressions have generated abundant results; next-generation sequencing technology has further boosted the number of variants and genes identified. Effective interpretation requires massive annotation and downstream analysis of these genome-wide results, a computationally challenging task. We developed the snpGeneSets package to simplify annotation and analysis of GWS results. Our package integrates local copies of knowledge bases for SNPs, genes, and gene sets, and implements wrapper functions in the R language to enable transparent access to low-level databases for efficient annotation of large genomic data. The package contains functions that execute three types of annotations: (1) genomic mapping annotation for SNPs an

SUBMITTER: Mei H 

PROVIDER: S-EPMC5144977 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature