buildDB: Build a chemical reference database table using rda files

In lauzikaite/massFlowR: LC-MS Data Pre-Processing

Description

Function generates a chemical reference database table from rda files in the selected directory (rda_dir).

Usage

buildDB(rda_dir = NULL, out_dir = NULL, peakgr_thr = 0, compound_thr = 0)

Arguments

rda_dir	character with absolute path to the directory with rda files.
out_dir	character with absolute path to the directory where database file should be written.
peakgr_thr	numeric specifying intensity threshold (100% BPI) for peaks in a chemical spectrum. If set to more than 0, peaks below will be removed.
compound_thr	numeric specifying intensity threshold (100% BPI) for peaks in all compound's chemical spectra. If set to more than 0, peaks below will be removed.

Details

Each rda file must be written for each chemical compond separately and contain a chem.file list, comprising the following four entries:

• header listing experimental details.

• id specifying chemical compound identity.

• reference

• analytical listing all detected peaks, which were built into chemical spectra (i.e. peak groups).

The database table contains columns: "peakid", "mz", "rt", "into", "chemid", "dbid", "dbname".

Value

Function returns generated database table and writes it to a csv file in the selected directory (out_dir).

See Also

annotateDS

lauzikaite/massFlowR documentation built on April 29, 2020, 9:45 a.m.