fastmart

The goal of fastmart is to speed up a subset of biomart queries by caching local, properly indexed sqlite databases.

Installation

You can install fastmart from R-Universe:

install.packages("fastmart", repos = "https://ropensci.r-universe.dev")

Or install the develeopment version from github:

# install.packages('remotes')
# remotes::install_github("selkamand/fastmart")
install.packages("fastmart", repos = c('https://selkamand.r-universe.dev', 'https://cloud.r-project.org'))

Quick start

The first time you use this package, you will need to initialise fastmart and cache the tables we need. This can be done as follows

library(fastmart)

# Initialise fastmart (creates a ~/.fastmart directory key databases will be stored)
fastmart_init()

# Cache the key tables
fastmart_cache_tables(GRCh = "37") 

You can now use any of the supported quick lookups

Available Functionality

Convert Gene IDs

Convert HGNC Symbols to ENSEMBL gene IDs

# Convert HGNC to Ensemble IDs
fastmart_convert_hgnc_to_ensembl('TBCE', chrom='1', start='235530675', end='235612283', GRCh = "37")
  # > ENSG00000116957.8

Annotate Gene with biotype

fastmart_annotate_biotype('ENSG00000282455.1')
#> IG_D_gene