MassArrayData-class: Class "MassArrayData"

In MassArray: Analytical Tools for MassArray Data

Description

A data structure containing MassArray data and associated information for a single amplicon

Objects from the Class

Objects can be created by calls of the form new("MassArrayData", sequence, file, verbose, fwd.tag, rev.tag, fwd.primer, rev.primer, strand, lower.threshold, upper.threshold, header, skip, sep, comment.char, fill, method, position, ...).

Slots

sequence:

Nucleotide sequence for unconverted amplicon

chr:

Chromosomal position of amplicon

start:

Chromosomal position of amplicon

end:

Chromosomal position of amplicon

strand:

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

fwd.tag:

Nucleotide tag sequence 5' of the forward primer

rev.tag:

T7-containing nucleotide tag sequence 5' of the reverse primer

fwd.primer:

Length (in bp) of forward primer

rev.primer:

Length (in bp) of reverse primer

lower.threshold:

Lower limit (in Da) of usable mass window (default: 1500)

upper.threshold:

Upper limit (in Da) of usable mass window (default: 7000)

fragments.T:

List containing objects of class MassArrayFragment, corresponding to the T-cleavage reaction for the amplicon on the specified strand

fragments.C:

List containing objects of class MassArrayFragment, corresponding to the C-cleavage reaction for the amplicon on the specified strand

samples:

List containing object of class MassArraySpectrum, each corresponding to spectral data from a single sample

groups:

List of the group name to which each sample belongs

CpG.data:

Matrix containing analyzed methylation data, where each row is a sample and each column is a CG dinucleotide site

CpG.data.combined:

Matrix containing methylation data combined from multiple objects (or collapsed from within a single object), where each row is a sample and each column is a CG dinucleotide site

Methods

\$

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

\$<-

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

[

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

initialize

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

Author(s)

Reid F. Thompson ([e-mail]), John M. Greally ([e-mail])

Examples

showClass("MassArrayData")

Example output

Class "MassArrayData" [package "MassArray"]

Slots:
                                                                              
Name:           sequence               chr             start               end
Class:         character         character           integer           integer
                                                                              
Name:             strand           fwd.tag           rev.tag        fwd.primer
Class:         character         character         character           numeric
                                                                              
Name:         rev.primer   lower.threshold   upper.threshold       fragments.T
Class:           numeric           numeric           numeric              list
                                                                              
Name:        fragments.C           samples            groups          CpG.data
Class:              list              list         character            matrix
                        
Name:  CpG.data.combined
Class:            matrix

MassArray documentation built on Nov. 8, 2020, 5:16 p.m.