getOSWData_: Extract data from OpenSwathWorkflow .osw results file
In singjc/mstools: OpenSWATH Mass Spectrometry Data Exploration

Description Usage Arguments Value Author(s)

This function can be used to extract information from the OSW results file obtained from running OpenSwathWorkflow

getOSWData_(
  oswfile,
  run_name = "",
  precursor_id = "",
  peptide_id = "",
  peptide_unmodified = "",
  peptide_modified = "",
  mod_peptide_id = c("", ""),
  mod_residue_position = "",
  peak_group_rank_filter = FALSE,
  report_top_single_result = FALSE,
  pep_list = "",
  mscore_filter = c(SCORE_ = 1),
  ipf_filter = "",
  ipf_score = FALSE,
  ms2_score = TRUE,
  decoy_filter = TRUE,
  inference_level = "peptide_query",
  mod_exclusion = NULL,
  mod_grouping = NULL,
  remove_KR_label = NULL
)

`oswfile`	A character vector of the absolute path and filename of the osw results file. (Must be .osw format)
`run_name`	A character vector for extraction of a specific run, this should be the same as the file name in the .OSW RUN table. (i.e. run_name='yanliu_I170114_016_PhosNoco4_SW.mzXML.gz', Default: ”)
`precursor_id`	A numeric value for a specific precursor id to extract information for. (Default: ”)
`peptide_id`	A numeric value for a specific peptide id to extract information for. (Default: ”)
`peptide_unmodified`	A string vector indicating a specific unmodified peptide sequence to extract information for. (Default: ”)
`peptide_modified`	A string vector indicating a specific modified peptide sequence to extract information for. (Default: ”)
`mod_peptide_id`	An array of two string vectors indicating a specific modified peptide sequence with both UniMod annotation and actual modification name to extract information for. I.e. c(ANS(Phos)SNSLK, ANS(UniMod:21)SNSLK) (Default: ”)
`mod_residue_position`	A numeric value indicating the position of a modification. (Default: ”)
`peak_group_rank_filter`	A Logical value for filtering OSW results by Peak-Group Rank of 1. (Default: FALSE)
`report_top_single_result`	A logical value indificating to keep only the results with the lowest m_score. (Default: TRUE)
`pep_list`	An arrary of string modified peptide sequences to extract information for. (Default: ”)
`mscore_filter`	A named numeric value to filter results by named q-value. (Default: ”) Options: SCORE_MS2, SCORE_IPF, SCORE_PEPTIDE. Example: c(SCORE_MS2=0.01)
`ipf_filter`	A numeric value to filter results by IPF PEP. (Default: ”)
`ipf_score`	A logical value to extract data using IPF Score results. (Default: FALSE)
`ms2_score`	A logical value to extract data using MS2 Score results. (Default: TRUE)
`decoy_filter`	A logical value to filter decoys out of final results. (Default: TRUE)
`mod_exclusion`	A vector of unimod record id modifications to exclude, and replace by nothing. Example: c("35")
`mod_grouping`	A dataframe contained uninod ids and random characters to group isomers by. Example: data.frame( record_id=c(4, 259, 267), rand_char_id="B", stringsAsFactors = F )
`remove_KR_label`	A vector of UniMod Ids to remove from Arginine or Lysine. Example: c("UniMod:259", "UniMod:267")