Package 'CentroidR' reference manual

Title:	CentroidR
Description:	CentroidR provides the infrastructure to centroid profile spectra.
Authors:	Adriano Rutz [aut, cre] (ORCID: <https://orcid.org/0000-0003-0443-9902>), Johannes Rainer [aut] (ORCID: <https://orcid.org/0000-0002-6977-7147>)
Maintainer:	Adriano Rutz <[email protected]>
License:	AGPL (>= 3)
Version:	0.0.0.9003
Built:	2026-06-09 11:06:11 UTC
Source:	https://github.com/adafede/CentroidR

Centroid an mzML file with configurable parameters

Description

This function processes an mzML file to apply centroiding with detailed controls for peak picking, smoothing, and noise estimation. It allows fine-tuning of MS1 and MS2 peak detection, optimizing spectral data analysis for various experimental needs.

Usage

centroid_one_file(
  file,
  pattern,
  replacement,
  min_datapoints_ms1 = 5L,
  min_datapoints_ms2 = 1L,
  mz_tol_da_ms1 = 0.0025,
  mz_tol_da_ms2 = 0.0025,
  mz_tol_ppm_ms1 = 5,
  mz_tol_ppm_ms2 = 5,
  mz_fun_ms1 = base::mean,
  mz_fun_ms2 = base::mean,
  int_fun_ms1 = base::max,
  int_fun_ms2 = base::max,
  mz_weighted = TRUE,
  time_domain = TRUE,
  intensity_exponent = 3
)
centroid_one_file(
  file,
  pattern,
  replacement,
  min_datapoints_ms1 = 5L,
  min_datapoints_ms2 = 1L,
  mz_tol_da_ms1 = 0.0025,
  mz_tol_da_ms2 = 0.0025,
  mz_tol_ppm_ms1 = 5,
  mz_tol_ppm_ms2 = 5,
  mz_fun_ms1 = base::mean,
  mz_fun_ms2 = base::mean,
  int_fun_ms1 = base::max,
  int_fun_ms2 = base::max,
  mz_weighted = TRUE,
  time_domain = TRUE,
  intensity_exponent = 3
)

Arguments

file

character(1). Path to the input mzML file. Must be a valid, accessible mzML format file.

pattern

character(1). Regular expression pattern to match in the input file path, used for modifying the output file path.

replacement

character(1). Replacement string for altering the output file path based on the pattern.

min_datapoints_ms1

integer(1). Minimum datapoints to be considered for MS1 data. Default: 5L.

min_datapoints_ms2

integer(1). Minimum datapoints to be considered for MS2 data. Default: 1L.

mz_tol_da_ms1

numeric(1). m/z tolerance in Daltons for MS1 data. Default: 0.0025.

mz_tol_da_ms2

numeric(1). m/z tolerance in Daltons for MS2 data. Default: 0.0025.

mz_tol_ppm_ms1

numeric(1). m/z tolerance in parts per million (ppm) for MS1. Default: 5.

mz_tol_ppm_ms2

numeric(1). m/z tolerance in parts per million (ppm) for MS2. Default: 5.

mz_fun_ms1

function. Function to aggregate m/z values within each peak group (MS1). Ignored if mz_weighted = TRUE. Default: base::mean.

mz_fun_ms2

function. Function to aggregate m/z values within each peak group (MS2). Ignored if mz_weighted = TRUE. Default: base::mean.

int_fun_ms1

function. Function to aggregate peak intensities within each peak group (MS1). Default: base::max.

int_fun_ms2

function. Function to aggregate peak intensities within each peak group (MS2). Default: base::max.

mz_weighted

logical(1). If TRUE, uses intensity-weighted mean for m/z value aggregation. Default: TRUE.

time_domain

logical(1). If TRUE, uses square root for m/z weighting (TRUE for TOF). Default: TRUE.

intensity_exponent

numeric(1). If mz_weighted=TRUE, the exponent of the intensity for m/z weighting. Default: 3.

Details

The function processes both MS1 and MS2 data with user-defined smoothing, peak-picking, and noise estimation. File path modifications are supported via pattern and replacement.

Value

logical(1). Returns TRUE if centroiding was successful, otherwise FALSE.

Author(s)

Johannes Rainer, Adriano Rutz

Package 'CentroidR'