read_study_design: Reading and Writing Study Design Tables

In PNNL-Comp-Mass-Spec/PNNL.DMS.utils: Tools for accessing PNNL's Data Management System

Reading and Writing Study Design Tables

Description

Fetches study design results from DMS. Checks that study design files are internally consistent. DMS functionality not useful outside of PNNL unless connected through VPN.

• path_to_study_design_from_DMS(): gets location of study design files from the DMS.

• read_study_design_from_DMS(): reads study design tables from the DMS data package folder.

• write_study_design_to_DMS(): writes study design tables to the DMS so that they can be accessed by others.

Usage

path_to_study_design_from_DMS(data_package_num)

read_study_design_from_DMS(data_package_num, useHTTP = FALSE)

write_study_design_to_DMS(data_package_num, study_design, overwrite = FALSE)

Arguments

data_package_num	(integer) data package number for DMS
useHTTP	(logical) whether to...
study_design	(list) study design files: fractions, samples, and references.
overwrite	(logical) whether to replace any existing study design tables when writing files.

Examples

if (is_PNNL_DMS_connection_successful()) {
  study_design <- read_study_design_from_DMS(3606)

  fractions  <- study_design$fractions
  samples    <- study_design$samples
  references <- study_design$references
}

PNNL-Comp-Mass-Spec/PNNL.DMS.utils documentation built on Jan. 20, 2025, 9:10 a.m.