Class "MassArrayFragment"

Description

A data structure containing information for a single fragment of an amplicon

Objects from the Class

Objects can be created by calls of the form new("MassArrayFragment", ID, sequence, assay.name, name, position, type, direction, extra, bisulfite.converted, assayable, primer, ...).

Slots

ID:

Unique integer indexing the fragment's position within a potential list of multiple fragments

assay.name:

(currently not supported)

name:

(currently not supported)

sequence:

Bisulphite converted nucleotide sequence of fragment

position:

Relative position of fragment within the amplicon

length:

Length (in bp) of fragment sequence

CpGs:

Number of CG dinucleotides contained within the fragment

MW:

Predicted molecular weight(s) of fragment, including methylated and unmethylated mass, adducts, etc.

collisions:

Number of fragments that share the same molecular weight as the current fragment

collision.IDs:

IDs of other fragments that share the same molecular weight as the current fragment

CG.collisions:

Number of CG-containing fragments that share the same molecular weight as the current fragment

CG.collision.IDs:

IDs of other CG-containing fragments that share the same molecular weight as the current fragment

type:

Specifies either 'T' or 'C' cleavage reaction

direction:

DNA strand used for fragment sequence (can be '+' or '-')

extra:

One of "5PPP-3P", "5OH", or "5PPP-3OH" (default)

bisulfite.converted:

Logical indicating whether the fragment sequence represents bisulfite converted sequence

assayable:

Logical indicating whether or not the fragment molecular weight is within the usable mass window

conversion.control:

Logical indicating whether or not the fragment is designated as a potential conversion control

required:

Logical indicating whether or not the fragment is designated as 'required' by the user

ignored:

Logical indicating whether or not the fragment is to be ignored

primer:

Logical indicating whether or not the fragment overlaps with primer or tagged sequence

Methods

$

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

$<-

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

initialize

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

Author(s)

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

See Also

See Also MassArrayData

Examples

showClass("MassArrayFragment")

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

Slots:
                                                                  
Name:                   ID          assay.name                name
Class:             integer           character           character
                                                                  
Name:             sequence            position              length
Class:           character             integer             integer
                                                                  
Name:                 CpGs                  MW          collisions
Class:             integer             numeric             integer
                                                                  
Name:        collision.IDs       CG.collisions    CG.collision.IDs
Class:                list             integer                list
                                                                  
Name:                 type           direction               extra
Class:           character           character           character
                                                                  
Name:  bisulfite.converted           assayable  conversion.control
Class:             logical             logical             logical
                                                                  
Name:             required             ignored              primer
Class:             logical             logical             logical
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>