getQuery {DIAlignR} | R Documentation |
Generate SQL query to fetch information from osw files.
getQuery( maxFdrQuery, oswMerged = TRUE, analytes = NULL, filename = NULL, runType = "DIA_Proteomics", analyteInGroupLabel = FALSE, identifying = FALSE )
maxFdrQuery |
(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 |
(string) as mentioned in RUN table of 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. |
identifying |
(logical) TRUE for the extraction of identifying transtions. (Default: FALSE) |
SQL query to be searched.
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2019) + GPL-3 Date: 2019-12-14