# Automated Functional Annotation of Genetic Variants and Linked Proxies

## Documentation for package ‘SNPannotator’ version 1.4.8

- 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
findSynonyms | Find variant synonyms from Ensembl
getConfigFile | Copy a sample configuration file
merge_annotations | Merge multiple inSilico annotation output objects and export to Excel
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