archiveDatabase: pull entire database (not counts) and save to output_dir for...

In cmatKhan/brentlabRnaSeqTools: A Collection of Functions to Interact with the Brentlab RNASeq Database

Description

saves both the individual tables, including counts, and the combined_df

Usage

archiveDatabase(
  database_host,
  database_name,
  database_user,
  database_password,
  output_dir,
  archive_counts_flag = TRUE
)

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
output_dir	where to deposit a subdirectory, named by todays date in this format: 20210407, with the tables and combined_df inside. eg a mounted local directory /mnt/htcf_lts/crypto_database_archive/ –> /lts/mblab/Crypto/rnaseq_data/crypto_database_archive
archive_counts_flag	boolean indicating whether or not to save the counts. default is TRUE

Value

None, writes a directory called <today's date> with tables and combined_df as .csv to output_dir

cmatKhan/brentlabRnaSeqTools documentation built on Nov. 17, 2021, 5:47 a.m.