getPrecursors {DIAlignR} | R Documentation |
Get a data-frame of analytes' transition_group_id, transition_ids, peptide_id and amino-acid sequences.
getPrecursors(fileInfo, oswMerged = TRUE, runType = "DIA_proteomics")
fileInfo |
(data-frame) Output of DIAlignR::getRunNames function. |
oswMerged |
(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet. |
runType |
(char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics". |
(data-frames) A data-frame having following columns:
transition_group_id |
(integer) a unique id for each precursor. |
transition_id |
(list) fragment-ion ID associated with transition_group_id. This is matched with chromatogram ID in mzML file. |
peptide_id |
(integer) a unique id for each peptide. A peptide can have multiple precursors. |
sequence |
(string) amino-acid sequence of the precursor with possible modifications. |
charge |
(integer) charge on the precursor. |
group_label |
(string) TODO Figure it out. |
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2019) + GPL-3 Date: 2019-04-06
getRunNames, fetchPrecursorsInfo
dataPath <- system.file("extdata", package = "DIAlignR") fileInfo <- DIAlignR::getRunNames(dataPath = dataPath) ## Not run: precursorsInfo <- getPrecursors(fileInfo, oswMerged = TRUE, runType = "DIA_proteomics") dim(precursorsInfo) # 322 6 ## End(Not run)