read_MSstats_from_MSFragger_job: Reading MSFragger-generated MSstats from PNNL's DMS as MSnSet...

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

Reading MSFragger-generated MSstats from PNNL's DMS as MSnSet object

Description

Function has only been tested with label-free intensity-based quantification data. It has not been tested with TMT data. MSstats.csv is an optional output file which needs to be specified in DMS settings file.

Usage

read_MSstats_from_MSFragger_job(
  data_package_num,
  param_file = NULL,
  settings_file = NULL,
  organism_db = NULL
)

Arguments

data_package_num	numeric or character; the Data Package ID in the DMS.
param_file	character; MSFragger parameter file. No need to specify this if there is only one parameter file associated with the jobs.
settings_file	character; MSFragger settings file. No need to specify this if there is only one settings file associated with the jobs.
organism_db	character; FASTA file name. This is the same as the Organism DB column. No need to specify this if there is only one FASTA file associated with the jobs.

Value

(MSnSet) MSnSet object of FragPipe LFQ results

Examples

if (is_PNNL_DMS_connection_successful()) {
  msnset <- read_MSstats_from_MSFragger_job(
    data_package_num = 4938,
    param_file = "MSFragger_Tryp_Dyn_MetOx_ProtNTermAcet_Stat_CysAlk_20ppmParTol.params",
    settings_file = "MSFragger_MatchBetweenRuns_Java80GB.xml",
    organism_db = "ID_008026_7A1842EC.fasta")
  show(msnset)
}

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