get_smarter_info: Get SMARTER Info

In cnr-ibba/r-smarter-api: Fetch SMARTER data through REST API

Get SMARTER Info

Description

Collect information about smarter database status and returns values in a list Cached token is used or a new token is generated if not provided when calling this function (see get_smarter_token for more information)

Usage

get_smarter_info(token = NULL)

Arguments

token

a string with a valid token

Value

a list object with SMARTER database information

About SMARTER database info endpoint

The info endpoint contains information about the status of the database

Keyword	Content
last_updated	when the SMARTER database was last updated
version	SMARTER database version (see the README in ftp site)
plink_specie	track the specie specific parameters to generate genotypes using plink
working_assemblies	the source of variant positions and genotypes

Those informations are required to understand if your genotypes are updated or not. For example, if the SMARTER database current version and last_updated are more recent than your genotype file, you could retrive information on samples not included in the genotype file. In such case, you have to download a more recent copy from SMARTER database from the FTP site. The plink_specie is a nested list which contains the plink species options used to generate the genotype data. if you want to modify a genotype file to be compatible to the SMARTER database you may want to use the same specie options

Examples

smarter_status <- get_smarter_info()
smarter_version <- smarter_status$version

cnr-ibba/r-smarter-api documentation built on Nov. 1, 2022, 4:24 a.m.