SpikeList-class {CALIB} | R Documentation |
A simple list-based class for storing red and green channel foreground and background intensities, spot area and concentrations for external control spike on spotted microarray.
Objects can be created by calls of the form new("SpikeList", spike)
where spike
is a list. In the CALIB package, SpikeList objects are normally generated by function
read.spike
.
Objects should contain the following list components:
R
:G
:Rb
:Gb
:RArea
:GArea
:RConc
:GConc
:genes
:All of the matrices should have the same dimensions.
Class "list"
, from data part.
Class "vector"
, by class "list"
.
This class inherits directly from class List, so any operation appropriate
for lists will work on objects of this class. In addition, SpikeList objects
can be subsetted
, combined
and merged
. SpikeList objects will return dimensions and
hence functions such as dim
, dimnames
,
nrow
and ncol
are defined.
Generic method show
is applied on SpikeList
,
so SpikeList will print in a compact way.
SpikeList objects are used on functions such as estimateParameter
or on some
other data visualization functions like plotSpikeHI
in the CALIB package.
Hui Zhao
the limma package
RGList
in limma package.