getOSWData_: Extract data from OpenSwathWorkflow .osw results file

Description Usage Arguments Value Author(s)

Description

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

Usage

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getOSWData_(
  oswfile,
  run_name = "",
  precursor_id = "",
  peptide_id = "",
  mod_peptide_id = c("", ""),
  mod_residue_position = "",
  peak_group_rank_filter = FALSE,
  pep_list = "",
  mscore_filter = "",
  ipf_filter = "",
  ipf_score = FALSE,
  ms2_score = TRUE,
  decoy_filter = TRUE
)

Arguments

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 string vector indicating a specific peptide 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)

pep_list

An arrary of string modified peptide sequences to extract information for. (Default: ”)

mscore_filter

A numeric value to filter results by MS2 q-value. (Default: ”)

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)

Value

A data.table containing OpenSwath Results information.

Author(s)

Justin Sing https://github.com/singjc


Roestlab/mstools documentation built on Jan. 25, 2020, 7:49 a.m.