getTransitions {DIAlignR} | R Documentation |
Get a list of data-frame of OpenSwath features that contains retention time, intensities, boundaries etc.
getTransitions( fileInfo, maxFdrQuery = 0.05, runType = "DIA_Proteomics", applyFun = lapply )
fileInfo |
(data-frame) output of |
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) yhis must be one of the strings "DIA_Proteomics", "DIA_Metabolomics". |
applyFun |
(function) value must be either lapply or BiocParallel::bplapply. |
(list of dataframes) each dataframe has following columns:
transition_group_id |
(integer) a unique id for each precursor. |
RT |
(numeric) retention time as in FEATURE.EXP_RT of osw files. |
intensity |
(list) of peak intensities as in FEATURE_TRANSITION.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. |
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2020) + GPL-3 Date: 2020-11-15
getRunNames, fetchTransitionsFromRun
dataPath <- system.file("extdata", package = "DIAlignR") fileInfo <- getRunNames(dataPath = dataPath) transitions <- getTransitions(fileInfo, maxFdrQuery = 1.00, runType = "DIA_Proteomics") dim(transitions[[2]]) # 938 8