Skip to contents

Querying Sample Status

query_sample_status.Rmd

The following packages are required:

Objective

This tutorial describes how to:

  1. Query the database for the status of a specific sample ID (or multiple sample IDs)
  2. Query the database for all sample IDs requiring further analysis

Check Status of Specific Samples

The function get_sample_status is helpful for when you already know the sample IDs about which you want more information. The function takes in one or more sample IDs and a connection and returns the following information:

  • id (unique identifier generated for the sample status table)
  • sample_id
  • status_code_id
  • status_code_name
  • comment
  • created_at
  • created_by

The function defaults to full_history = FALSE, showing you only the current status of the sample. If you want the full history of a sample, you can change the argument to full_history = TRUE.

con <- grunID::gr_db_connect()

# find the status of a specific sample "DER23_1_C_4" without the full history
grunID::get_sample_status(con, "DER23_1_C_4", full_history = FALSE)

# find the status of a specific sample "DER23_1_C_4" WITH the full history
grunID::get_sample_status(con, "DER23_1_C_4", full_history = TRUE)

Get a List of All Samples Needing Analysis

If you don’t have a specific sample ID in mind but want to know which samples in the database need further assays or clarification, you can use the function get_samples_needing_action. This function produces a list of Sample IDs organized into the following categories:

  • needs_ots_16
  • repeat_ots_28
  • repeat_ots_16
  • potential_heterozygotes
# produce a list of Sample IDs organized by the analysis required
grunID::get_samples_needing_action(con)