get_mz_table: get_mz_table

In YasinEl/mzRAPP: Benchmark Dataset Generation and Non-Targeted Data Pre-Processing Assessment

get_mz_table

Description

This is basically a wrapper-function around the enviPat package. It takes a table with columns "molecule", "SumForm_c" and "main_adduct" and calculates theoretical m/z values and abundances for isotopologues down to a user-defined abundance threshold.

Usage

get_mz_table(
  DT,
  instrumentRes,
  RelInt_threshold = 0.05,
  stick_method = "intensoid",
  adducts,
  isotopes,
  screening_adducts = NULL
)

Arguments

DT	data.table with columns "molecule", "SumForm_c", "adduct_c". Additional columns with "user.rtmin", and "user.rtmax" (start and end times of peaks in seconds won't be required by this, but the next function in the mzRAPP pipeline so it is recommended to add them already here.) (see details)
instrumentRes	data frame with mz vs resolution dependence (see resolution_list) e.g. "resolution_list$'OTFusion,QExactiveHF_120000@200'"
RelInt_threshold	relative abundance of the lowest isotopologue to be considered as percentage
stick_method	method that should be used to calculate discrete m/z values from calculated profile pattern e.g. "intensoid" (see vdetect)
adducts	data frame containing adducts (see adducts)
isotopes	data frame containing isotopes (see isotopes)
screening_adducts	vector of adduct names to be added for all molecules (if not already in the provided DT)

Details

Make sure that molecular formulas in column "SumForm_c" only contain valid molecular formulas as described in check_chemform. Otherwise, the function might never complete. Additional columns in DT will be retained in the output of the function. However, the column names "adduct", "isoab", "formula", "charge" and "mz" are reserved.

Value

data.table with columns "molecule", "formula", "adduct", "charge", "m/z" and "abundance"

YasinEl/mzRAPP documentation built on Feb. 18, 2024, 11:49 a.m.