buildDB: Build a chemical reference database table using rda files

Description Usage Arguments Details Value See Also

View source: R/functions-buildDB.R

Description

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

Usage

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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:

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 Dec. 16, 2019, 6:01 p.m.