lapisR - Retrieving data from LAPIS

lapisR provides functions for retrieving data from various LAPIS endpoints. These include functions requesting database statistics, sets of sequences and their metadata, sets of mutations or insertions, and sequence alignments.

Installation

library(devtools)
install_github("GenSpectrum/lapisR")

Usage

Session initialization

Sessions can be initialized with or without an access key. They can also be set to expire in case the database receives an update.

Example:

session <- lapisR::initialize("https://lapis.cov-spectrum.org/gisaid/v2", expireOnUpdate = TRUE, accessKey="myKey")

Database statistics

Aggregated data can be retrieved using the getAgregated function. Various filters can be applied. Valid filter keys for a particular session can be found with getFilters(session).

Example:

getAggregated(session, fields=c("country"), date = '2020-05-05')

Sequences

Nucleotide sequences can be obtained in FASTA format with the getNucleotideSequence function, either as string or as compressed or uncompressed file.

Example:

getNucleotideSequences(session, country = "Switzerland", date = '2020-05-05', limit = 10, downloadAsFile = TRUE, compression = 'gzip', out = 'mySequences')

Metadata

Sequence metadata can be retreived with getDetails.

Example:

getDetails(session, country = "Switzerland", date = '2020-05-05', limit = 10)

Mutations / Insertions

Nucleotide and amino acid mutations or insertions can be retreived with getNucleotideMutations, getNucleotideInsertions, getAminoAcidMutations, and getAminoAcidInsertions.

Example:

getNucleotideMutations(session, region = "Europe", minProportion = 0.1, limit = 100)

Alignments

Nucleotide and amino acid sequence alignments can be obtained with the getNucleotideAlignment and getAminoAcidAlignment functions, as string or as compressed or uncompressed FASTA file.

Example:

getAminoAcidAlignment(session, country = "Switzerland", date = '2020-05-05', limit = 10, downloadAsFile = TRUE, out = 'myAlignment')