Skip to contents

Convenience function to pull a single table

Usage

getTable(
  database_host,
  database_name,
  database_user,
  database_password,
  tablename
)

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

tablename

name of the table you wish to pull. Must have correct capitalization. I have attempted to make the camelCase consistent, eg bioSample, rnaSample

Value

a single table as a dataframe