c19.genomic.data {covid19.analytics}

function to obtain genomic data from SARS-CoV-2019

Description

function to obtain genomic data from SARS-CoV-2019

Usage

c19.genomic.data(src = "livedata", accOnly = TRUE)

Arguments

src

argument to indicate what sources are going to be used for retrieving the data: "livedata", "repo" or "local" 'livedata' will access NCBI servers to acquire the latest possible data, this may incur in significant longer times 'repo' will access an updated replica of the data from a github repository (faster but not necessarily upto the latest udpates) 'local' will access previously archived records within teh package (fastest but not updated)

accOnly

boolean indicator for getting only accession codes or whole records

Value

a list containing reference genome, annotation data, nucleotides, proteins and list of SRA runs