Class "MassArraySpectrum"

Description

A data structure containing MassArray spectral data for a single sample

Objects from the Class

Objects can be created by calls of the form new("MassArraySpectrum", sample, rxn, strand, peaks, quality.conversion, quality.spectra, quality.primerdimer, quality.contaminant, quality.adducts, ...).

Slots

sample:

Sample name

rxn:

Cleavage reaction (either 'T' or 'C')

strand:

DNA strand for amplicon (either '+' or '-')

peaks:

List containing objects of class MassArrayPeak

quality.conversion:

Overall level(s) of remnant unconverted cytosines, as measured by one or more conversion controls

quality.spectra:

(currently not supported)

quality.primerdimer:

(currently not supported)

quality.contaminant:

(currently not supported)

quality.adducts:

Overall ratio(s) of Na and/or K adduct peak heights to expected peak heights

Methods

$

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

$<-

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

initialize

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

Author(s)

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

See Also

See Also MassArrayData

Examples

showClass("MassArraySpectrum")

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/MassArraySpectrum-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MassArraySpectrum-class
> ### Title: Class "MassArraySpectrum"
> ### Aliases: MassArraySpectrum-class $,MassArraySpectrum-method
> ###   $<-,MassArraySpectrum-method initialize,MassArraySpectrum-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("MassArraySpectrum")
Class "MassArraySpectrum" [package "MassArray"]

Slots:
                                                                  
Name:               sample                 rxn              strand
Class:           character           character           character
                                                                  
Name:                peaks  quality.conversion     quality.spectra
Class:                list             numeric             numeric
                                                                  
Name:  quality.primerdimer quality.contaminant     quality.adducts
Class:             numeric             numeric             numeric
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>