prepare_peaks: Prepare list of peaks data into a data.frame

In ismaRP/MALDIpqi: Estimate Parchment Glutamine Index from MALDI-TOF datasets

Prepare list of peaks data into a data.frame

Description

Prepare list of peaks data into a data.frame

Usage

prepare_peaks(
  peaks,
  n_isopeaks,
  peptides_user = NULL,
  int_column = "intensity",
  norm_func = NULL,
  q2e = NULL
)

Arguments

peaks	List of peaks matrix. Names are used as spectra name
n_isopeaks	Number of isotopic peaks
peptides_user	A dataframe with peptide information. It must contain at least 3 columns, pep_number or ID, mass, sequence and h_hyp (# of hydroxyprolines). IF NULL, default are used, see details.
int_column	Columns in peaks with the intensity to be used
norm_func	Function to normalize the intensities of the isotopic envelope
q2e	If provided, it adds the theoretical isotopic distribution of peptides with this extent of deamidation

Details

The default peptides are the ones from Nair et al. (2022). The paper contains the details on the preprocessing procedure.

Value

A data.frame with isotopic peaks detected from data, theoretical isotopic envelopes for 1 and 2 deamidations and other associated data.

ismaRP/MALDIpqi documentation built on Feb. 14, 2025, 8:28 a.m.