getOswFiles: Get list of peptides and their chromatogram indices.
In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description Usage Arguments Value Author(s) See Also Examples

This function reads all osw and mzml files in the directories at dataPath. It selects analytes which has associated features with m-score < maxFdrQuery. For these analytes it fetches chromatogram indices by matching transition_id(osw) with chromatogramID(mzml).

getOswFiles(
  fileInfo,
  mzPntrs,
  maxFdrQuery = 0.05,
  analyteFDR = 0.01,
  oswMerged = TRUE,
  analytes = NULL,
  runType = "DIA_proteomics",
  analyteInGroupLabel = FALSE
)

`mzPntrs`	A list of mzRpwiz. FALSE for fetching analytes as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
`maxFdrQuery`	(numeric) A numeric value between 0 and 1. It is used to filter features from osw file which have SCORE_MS2.QVALUE less than itself.
`analyteFDR`	(numeric) Not used.
`oswMerged`	(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
`analytes`	(string) analyte is as PRECURSOR.GROUP_LABEL or as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
`runType`	(char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".
`analyteInGroupLabel`	(logical) TRUE for getting analytes as PRECURSOR.GROUP_LABEL from osw file.
`dataPath`	(char) path to mzml and osw directory.
`filenames`	(data-frame) column "filename" contains RUN table from osw files. column "runs" contain respective mzML names without extension. To get filenames use DIAlignR::getRunNames function.

(data-frames) Data-frame has following columns:

`transition_group_id`	(string) it is either fetched from PRECURSOR.GROUP_LABEL or a combination of PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
`RT`	(numeric) retention time as in FEATURE.EXP_RT of osw files.
`delta_rt`	(numeric) as in FEATURE.DELTA_RT of osw files.
`assay_RT`	(numeric) library retention time as in PRECURSOR.LIBRARY_RT of osw files.
`Intensity`	(numeric) peak intensity as in FEATURE_MS2.AREA_INTENSITY of osw files.
`leftWidth`	(numeric) as in FEATURE.LEFT_WIDTH of osw files.
`rightWidth`	(numeric) as in FEATURE.RIGHT_WIDTH of osw files.
`peak_group_rank`	(integer) rank of each feature associated with transition_group_id.
`m_score`	(numeric) q-value of each feature associated with transition_group_id.
`chromatogramIndex`	(integer) Index of chromatogram in mzML file.
`transition_ids`	(integer) fragment-ion ID associated with transition_group_id. This is matched with chromatogram ID in mzML file.

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-13

getRunNames

dataPath <- system.file("extdata", package = "DIAlignR")
filenames <- getRunNames(dataPath = dataPath)
## Not run: 
mzPntrs <- getMZMLpointers(filenames)
oswFiles <- getOswFiles(filenames, mzPntrs, analyteInGroupLabel = TRUE)
rm(mzPntrs)

## End(Not run)