annotateDS-massFlowAnno-method: Annotate dataset using chemical reference database.

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

Description

Method annotates a dataset using a chemical reference database. Peak-groups, or Pseudo Chemical Spectra (PCS), in the dataset are compared with the peak-groups representing reference compounds in the database. PCS are annotated using dot-product estimation between the spectra of the PCS and the corresponding chemical in the database.

Usage

## S4 method for signature 'massFlowAnno'
annotateDS(
  object,
  db_file = NULL,
  out_dir = NULL,
  mz_err = 0.01,
  rt_err = 10,
  ncores = 2
)

Arguments

object	massFlowAnno class object.
db_file	character for absolute path to the csv file of the chemical reference database, built using buildDB function.
out_dir	character specifying desired directory for output.
mz_err	numeric specifying the window for peak matching in the MZ dimension. Default set to 0.01.
rt_err	numeric specifying the window for peak matching in the RT dimension. Default set to 10 (sec).
ncores	numeric for number of parallel workers to be used. Set 1 for serial implementation. Default set to 2.

Value

Method writes an updated dataset table with columns 'chemid', 'dbname', and 'similarity', indicating matched chemical reference standards from the database. Column 'similarity' indicates the stringth of spectral similarity between the PCS and the corresponding chemical compound, ranging from 0 to 1.

See Also

buildDB, buildANNO

lauzikaite/massflowR documentation built on April 27, 2020, 5:32 p.m.