getQuery: Generate SQL query to fetch information from osw files.

In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Generate SQL query to fetch information from osw files.

Description

Generate SQL query to fetch information from osw files.

Usage

getQuery(
  maxFdrQuery,
  oswMerged = TRUE,
  analytes = NULL,
  filename = NULL,
  runType = "DIA_Proteomics",
  analyteInGroupLabel = FALSE,
  identifying = FALSE
)

Arguments

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)

Value

SQL query to be searched.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-14

shubham1637/DIAlignR documentation built on March 29, 2023, 8:45 p.m.