Get the combined metadata as a tibble from a remote database
getMetadata.RdJoin the biosample, rnasample, s1sample, s2sample, library, fastqFiles and qualityAssessment tables (in that order, left joins) and return the result as a tibble
Arguments
- database_host
if connecting to a database hosted on AWS, it might be something like ec2-54-83-201-96.compute-1.amazonaws.com
- database_name
name of the database, eg for cryptococcus kn99, the database might be named kn99_database. Check with the documentation, whoever set up the database, or get into the server and check directly
- database_user
a user of the actual database, with some level of permissions. You'll need to check with the database maintainer for this. It is suggested that you use a .Renviron file in your local project (make sure it is completely ignored by git, R, etc) to store this info
- database_password
password to the database user. You'll need to check with the database maintainer for this. It is suggested that you use a .Renviron file in your local project (make sure it is completely ignored by git, R, etc) to store this info
Note
for information on using R environmental files, see https://support.rstudio.com/hc/en-us/articles/360047157094-Managing-R-with-Rprofile-Renviron-Rprofile-site-Renviron-site-rsession-conf-and-repos-conf