Apply Peak Picking

Functions to perform peak picking on the data:

• apply_peak_picking

  • Wrapper to perform peak picking with any of the methods

• apply_peak_picking.cw

  • Peak picking with the CentWave method

• apply_peak_picking.mf

  • Peak picking with the Massifquant method

• apply_peak_picking.mq

  • Peak picking with the MatchedFilter method

Usage

apply_peak_picking(data, method = c("cw", "mf", "mq"), cores = 1, ...)

apply_peak_picking.cw(
  data,
  BPPARAM,
  ppm = 25,
  p_width = c(20, 50),
  snt = 3,
  noise = 1e+06,
  prefilter = c(1, 100),
  mz_diff = 0.001,
  ...
)

apply_peak_picking.mq(
  data,
  BPPARAM,
  ppm = 25,
  p_width = c(20, 50),
  snt = 3,
  noise = 1e+06,
  prefilter = c(1, 100),
  mz_diff = 0.001,
  ...
)

apply_peak_picking.mf(
  data,
  BPPARAM,
  bin = 0.1,
  fwhm = 30,
  sigma = 12.72,
  max = 10,
  steps = 2,
  ...
)

Arguments

data

An MSnExp object in centroid mode.

method

Character. Specifies the peak picking method. Options include 'cw' for CentWave, 'mq' for Massifquant, and 'mf' for MatchedFilter.

BPPARAM

BiocParallelParam-class object. Specifies the parallel processing parameters. Default is SnowParam with 4 workers.

ppm

Numeric. Specifies the parts per million for m/z tolerance. Additional parameters include p_width, snt, noise, prefilter, mz_diff, bin, fwhm, sigma, max, and steps, each with specific roles in peak picking.

p_width

Minium and maximum allowed peak width.

snt

Minimum signal-to-noise threshold allowed.

noise

Noise threshold.

prefilter

Prefilter step cutoff (c(k, I)). Mass will be retained if they contain at least k peaks with intensity >= I.

Value

MSnExp-class object after applying peak picking.

Details

Apply Peak Picking Function to apply peak picking parameters on a data subset