adductSpec-class: AdductSpec class

Description Usage Format Value Slots Methods Author(s)

Description

The AdductSpec class contains dynamic noise filtered composite MS/MS spectra and their corresponding MS1 scan isotopic patterns. Produced by adductSpecGen() from mzXML files.

Usage

1
x

Format

An object of class NULL of length 0.

Value

dynamic noise filtered composite MS/MS spectra and their corresponding MS1 scan isotopic patterns

Slots

adductMS2spec

list of adduct MS2 spectras

groupMS2spec

list of group MS2 spectras

metaData

dataframe of metadata from mzXML

aaResSeqs

matrix of amino acid sequences

specPepMatches

list of spectra peptide matches

specPepCompSpec

list of comp spectra peptide matches

sumAdductType

dataframe of adduct types

Peptides

dataframe of peptides under study

rtDevModels

list of rtDevModels

targetTable

dataframe target table

file.paths

character of file path

Parameters

dataframe of parameters

Methods

c

signature(object = "AdductSpec"): Concatenates the spectra information.

Specfile.paths

signature(object = "AdductSpec"): Accesses the file paths.

adductMS2spec

signature(object = "AdductSpec"): Accesses the adduct MS2 spectral information.

metaData

signature(object = "AdductSpec"): Accesses the scan metadata.

Parameters

signature(object = "AdductSpec"): Accesses the user parameters.

groupMS2spec

signature(object = "AdductSpec"): Accesses the spectral information for the grouped MS2 spectra.

rtDevModels

signature(object = "AdductSpec"): Accesses the retention time deviation models.

sumAdductType

signature(object = "AdductSpec"): Accesses the total adduct types.

Peptides

signature(object = "AdductSpec"): Accesses the peptide information.

specPepMatches

signature(object = "AdductSpec"): Accesses the peptide matches in the spectra.

Author(s)

JL Hayes jlhayes1982@gmail.com


JosieLHayes/adductomicsR documentation built on May 5, 2019, 9:43 p.m.