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

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.

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)
}