pnnl_dms_utils: Utilities for interacting with PNNL DMS

In vladpetyuk/PlexedPiper: Pipeline for isobaric quantification.

Description

Fetches results of different data analysis tools. Not useful outside of PNNL unless connected through VPN. Works on windows out of the box. To make it work on Mac/Linux FreeTDS needs to be installed. Mac/Linux functionality is not well tested.

• get_dms_job_records(): returns job records given variety keyword patterns

• get_tool_output_files_for_job_number(): returns the output of the tool given tool name and file pattern

• get_output_folder_for_job_and_tool(): returns the path given job id and tool name

• get_AScore_results(): returns Ascore results given data packge number

• get_job_records_by_dataset_package(): returns job records given data packge number

• get_results_for_multiple_jobs(): returns concatenated results given job numbers

• get_results_for_multiple_jobs.dt(): returns results as concatenated data.table given job numbers

• get_results_for_single_job(): returns results given job number

• get_results_for_single_job.dt(): returns results as data.table given job number

Usage

is_PNNL_DMS_connection_successful()

get_dms_job_records(
  jobs = NULL,
  datasetPttrn = "",
  experimentPttrn = "",
  toolPttrn = "",
  parPttrn = "",
  settingsPttrn = "",
  fastaPttrn = "",
  proteinOptionsPttrn = "",
  intrumentPttrn = ""
)

get_tool_output_files_for_job_number(
  jobNumber,
  toolName,
  filePattern,
  mostRecent = TRUE
)

get_output_folder_for_job_and_tool(jobNumber, toolName, mostRecent = TRUE)

get_AScore_results(dataPkgNumber)

get_job_records_by_dataset_package(dataPkgNumber)

get_results_for_multiple_jobs(jobRecords)

get_results_for_multiple_jobs.dt(jobRecords)

get_results_for_single_job(pathToFile, fileNamePttrn)

get_results_for_single_job.dt(pathToFile, fileNamePttrn)

path_to_FASTA_used_by_DMS(data_package_number)

get_study_design_by_dataset_package(dataPkgNumber)

Arguments

jobs	(integer) DMS job ID
mostRecent	(logical) only most recent or all output files
dataPkgNumber	(interger) data package id
mtdbName	(string) name of mass tag database
xPttrn	(string) substrings for names of dataset, experiment, tool, parameter file, settings file, fasta file, protein options, instrument name

Examples

get_output_folder_for_job_and_tool(863951, "DTA_Refinery")

vladpetyuk/PlexedPiper documentation built on June 24, 2021, 8:59 a.m.