Class "MassArrayPeak"

Description

A data structure containing information and data for a single peak from a single spectrum

Objects from the Class

Objects can be created by calls of the form new("MassArrayPeak", ID, MW.theoretical, MW.actual, probability, SNR, height, sample.intensity, ref.intensity, sequence, adduct, type, charge, collisions, components, missing, new, ...).

Slots

ID:

Peak ID inicating indexed position within a potentially large list of peaks

MW.theoretical:

Expected molecular weight of peak based on nucleotide sequence

MW.actual:

Observed molecular weight from experimental data

probability:

Object of class "numeric" ~~

SNR:

Signal-to-noise ratio

height:

Raw peak height

sample.intensity:

Raw sample intensity

ref.intensity:

Object of class "numeric" ~~

sequence:

Nucleotide composition or sequence(s) corresponding to peak

adduct:

One of 'Na', 'K', or ” indicating whether or not peak represents a salt adduct of another expected peak

type:

Object of class "character" ~~

charge:

Degree of ionization of fragment (default is '1' indicating a single positive charge per fragment)

collisions:

Number of peaks that share the same molecular weight as the current peak

components:

Number of fragments expected to give rise to a peak of this molecular weight

missing:

Logical indicating whether or not the expected peak is missing from the spectral data

new:

Logical indicating whether or not the observed peak is unexpected given the amplicon sequence

Methods

$

signature(x = "MassArrayPeak"): ...

$<-

signature(x = "MassArrayPeak"): ...

initialize

signature(.Object = "MassArrayPeak"): ...

Author(s)

Reid F. Thompson (rthompso@aecom.yu.edu), John M. Greally (jgreally@aecom.yu.edu)

See Also

See Also MassArrayData

Examples

showClass("MassArrayPeak")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MassArray)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MassArray/MassArrayPeak-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MassArrayPeak-class
> ### Title: Class "MassArrayPeak"
> ### Aliases: MassArrayPeak-class $,MassArrayPeak-method
> ###   $<-,MassArrayPeak-method initialize,MassArrayPeak-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("MassArrayPeak")
Class "MassArrayPeak" [package "MassArray"]

Slots:
                                                                          
Name:                ID   MW.theoretical        MW.actual      probability
Class:          integer          numeric          numeric          numeric
                                                                          
Name:               SNR           height sample.intensity    ref.intensity
Class:          numeric          numeric          numeric          numeric
                                                                          
Name:          sequence           adduct             type           charge
Class:        character        character        character          integer
                                                                          
Name:        collisions       components          missing              new
Class:          integer          integer          logical          logical
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>