read_msfragger_data_from_DMS: Reading MSFragger output from PNNL's DMS

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

Reading MSFragger output from PNNL's DMS

Description

Reading MSFragger output from PNNL's DMS

Usage

read_msfragger_data_from_DMS(
  data_package_num,
  param_file = NULL,
  settings_file = NULL,
  organism_db = NULL,
  assume_inference = FALSE
)

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.
assume_inference	logical; If TRUE then takes the Protein column as protein ids that passed the inference step. Otherwise, the function will take both Protein and ⁠Mapped Proteins⁠ and report all of them on separate rows for the matching peptides.

Value

(MSnID) MSnID object

Examples

if (is_PNNL_DMS_connection_successful()) {
  msnid <- read_msfragger_data_from_DMS(4139)
  show(msnid)
}

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