Package 'CentroidR' reference manual

Title:	CentroidR
Description:	CentroidR provides the infrastructure to centroid profile spectra.
Authors:	Adriano Rutz [aut, cre] , Johannes Rainer [aut]
Maintainer:	Adriano Rutz <[email protected]>
License:	GPL (>= 3)
Version:	0.0.0.9000
Built:	2025-03-11 15:28:23 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 = 2L,
  min_datapoints_ms2 = 1L,
  mz_tol_da_ms1 = 0.002,
  mz_tol_da_ms2 = 0.005,
  mz_tol_ppm_ms1 = 5,
  mz_tol_ppm_ms2 = 10,
  mz_fun = base::mean,
  int_fun = base::sum,
  mz_weighted = TRUE
)
centroid_one_file(
  file,
  pattern,
  replacement,
  min_datapoints_ms1 = 2L,
  min_datapoints_ms2 = 1L,
  mz_tol_da_ms1 = 0.002,
  mz_tol_da_ms2 = 0.005,
  mz_tol_ppm_ms1 = 5,
  mz_tol_ppm_ms2 = 10,
  mz_fun = base::mean,
  int_fun = base::sum,
  mz_weighted = TRUE
)

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)` (default: `2L`) Minimum datapoints to be considered for MS1 data.
`min_datapoints_ms2`	`integer(1)` (default: `1L`) Minimum datapoints to be considered for MS2 data.
`mz_tol_da_ms1`	`numeric(1)` (default: `0.002`) m/z tolerance in Daltons for MS1 data.
`mz_tol_da_ms2`	`numeric(1)` (default: `0.005`) m/z tolerance in Daltons for MS2 data.
`mz_tol_ppm_ms1`	`numeric(1)` (default: `5`) m/z tolerance in parts per million (ppm) for MS1.
`mz_tol_ppm_ms2`	`numeric(1)` (default: `10`) m/z tolerance in parts per million (ppm) for MS2.
`mz_fun`	`function` (default: `base::mean`) Function to aggregate m/z values within each peak group. Ignored if `mz_weighted = TRUE`.
`int_fun`	`function` (default: `base::sum`) Function to aggregate peak intensities within each peak group.
`mz_weighted`	`logical(1)` (default: `TRUE`) If `TRUE`, uses intensity-weighted mean for m/z value aggregation.

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'