getOswFiles {DIAlignR} | R Documentation |
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
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)