fetchAnalytesInfo {DIAlignR} | R Documentation |
Get a data-frame of analytes' transition_group_ids, their OpenSwath features, chromatogram indices and associated FDR-scores.
fetchAnalytesInfo( oswName, maxFdrQuery, oswMerged, analytes, filename, runType, analyteInGroupLabel = FALSE )
oswName |
(char) path to the 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. |
oswMerged |
(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet. |
analytes |
(vector of strings) transition_group_ids for which features are to be extracted. analyteInGroupLabel must be set according the pattern used here. |
filename |
(data-frame) Should be from the RUN.FILENAME column from osw files. |
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. FALSE for fetching analytes as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file. |
(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. |
filename |
(string) as mentioned in RUN table of osw files. |
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. |
transition_id |
(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 <- DIAlignR::getRunNames(dataPath = dataPath) oswName <- paste0(dataPath,"/osw/merged.osw") ## Not run: analytesInfo <- fetchAnalytesInfo(oswName, maxFdrQuery = 0.05, oswMerged = TRUE, analytes = c("19051_KLIVTSEGC[160]FK/2"), filename = filenames$filename[2], runType = "DIA_proteomics", analyteInGroupLabel = TRUE) analytesInfo <- fetchAnalytesInfo(oswName, maxFdrQuery = 0.05, oswMerged = TRUE, analytes = c("IHFLSPVRPFTLTPGDEEESFIQLITPVR_3"), filename = filenames$filename[3], runType = "DIA_proteomics", analyteInGroupLabel = FALSE) ## End(Not run)