getOswAnalytes {DIAlignR} | R Documentation |
Get a data-frame of analytes, their chromatogram indices and associated FDR-scores.
getOswAnalytes( fileInfo, oswMerged = TRUE, analyteInGroupLabel = FALSE, maxFdrQuery = 0.05, runType = "DIA_Proteomics" )
oswMerged |
(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet. |
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. |
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. |
runType |
(char) This must be one of the strings "DIA_Proteomics", "DIA_Metabolomics". |
dataPath |
(char) path to xics 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 |
(A list of data-frames) Each 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. |
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 <- getRunNames(dataPath = dataPath) ## Not run: oswFiles <- getOswAnalytes(dataPath = dataPath, filenames = filenames, analyteInGroupLabel = TRUE) oswFiles[["run0"]][1,] oswFiles <- getOswAnalytes(dataPath = dataPath, filenames = filenames, analyteInGroupLabel = FALSE) oswFiles[["run0"]][1,] ## End(Not run)