Complist-class: Class '"Complist"'

In thomasp85/pepmaps: Create peptide maps by merging xcms (and CAMERA) with MassAI

Description

This class combines Peaklist object with different types of ID lists (only PepID objects currently supported), matching ID to the quantified peakgroups

Objects from the Class

Objects can be created using the complist constructor which automatically links ID's to peakgroups. Furthermore the wrapper function createComplist will also output a Complist object. Objects can also be created by calls of the form new("Complist", ...).

Slots

peakID:

A logical data frame giving the peakgroups that have been matched to ID

IDindex:

A list giving the mathc between ID and peakgroups

pepID:

The PepID object used

raw:

A matrix containing the intensities of each sample for all peakgroups

Sample.info:

A data frame containing information on each sample

Peak.info:

A data frame containing chromatographic information for each peak group

annotated:

TRUE/FALSE giving whether CAMERA analysis has been performed on data

parameters:

A Parameters object containing all different analysis parameters used

Extends

Class "Peaklist", directly.

Methods

getIntensity

signature(object = "Complist"): Extract intensity for all ID'ed peak groups or a specific ID

plotPeak

signature(object = "Complist"): Plot EIC for a given ID

Author(s)

Thomas Dybdal Pedersen

See Also

complist

thomasp85/pepmaps documentation built on May 31, 2019, 11:15 a.m.