Automated Functional Annotation of Genetic Variants and Linked Proxies

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Documentation for package ‘SNPannotator’ version 1.4.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

annotate_shiny	Run the annotation pipeline on a list of variants from shiny app
demo_annotation	Demo run of the annotation pipeline
EnsemblDatabases	List population from human database (1000 Genomes project)
EnsemblReleases	data release available on this REST server.
findGenomicPos	Query GTEx portal for Variant's genomic position based on rsID Retrieves variant information from the GTEx portal using either an rsID or a variant ID formatted as 'CHR_POS_REF_ALT'. If an rsID is provided, the function returns the corresponding genomic positions in both GRCh37 and GRCh38 builds. When searching for an rsID based on genomic position, the position parameter should be specified according to the GRCh38 reference genome.
findPairwiseLD	Computes and returns LD values between the given variants.
findProxy	Finds variants in high LD
findRSID	Query Ensembl for variant information based on genomic position
getConfigFile	Copy a sample configuration file
mergeResultFiles	Merge multiple output files
pingEnsembl	Checks if the service is alive
run_annotation	Run the annotation pipeline on a list of variants
run_stringdb_annotation	Analyze STRING DB Interactions and perform functional enrichment