Reading MSFragger output from PNNL's DMS

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.

(MSnID) MSnID object

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