getTransitionScores_: Extract Transition Information from .osw results file

In singjc/mstools: OpenSWATH Mass Spectrometry Data Exploration

Description

This function can be used to extract Transition Id and Transition Posterior Error Probability information from the OSW results file obtained from running OpenSwathWorkflow

Usage

getTransitionScores_(
  oswfile,
  run_name,
  precursor_id = "",
  peptide_id = "",
  mod_peptide_id = c("", ""),
  detecting = TRUE,
  identifying = 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 name as the file name in the .OSW RUN table.
precursor_id	A numeric value for a specific precursor id to extract information for. (Default: ”)
peptide_id	A string vector indicatig 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: ”)

Value

A data.table containing Transition IDs and Transition Posterior Error Probabilities, and other useful information. Similar to getOSWData.R.

Author(s)

Justin Sing https://github.com/singjc

singjc/mstools documentation built on June 28, 2020, 8:10 p.m.