Description Required Components Optional Components Methods Author(s) See Also Examples
A list-based S4 classes for storing expression values (E-values), for example for a set of one-channel microarrays or a set of RNA-seq samples.
EListRaw
holds expression values on the raw scale.
EList
holds expression values on the log scale, usually after background correction and normalization.
EListRaw
objects are often created by read.maimages
, while
EList
objects are often created by normalizeBetweenArrays
or by voom
.
Alternatively, an EList
object can be created directly by new("EList",x)
, where x
is a list.
These classes contains no slots (other than .Data
), but objects should contain a list component E
:
E
numeric matrix containing expression values.
In an EListRaw
object, the expression values are unlogged, while in an EList
object, they are log2 values.
Rows correspond to probes and columns to samples.
Optional components include:
Eb
numeric matrix containing unlogged background expression values, of same dimensions as E
. For an EListRaw
object only.
weights
numeric matrix of same dimensions as E
containing relative spot quality weights. Elements should be non-negative.
other
list containing other matrices, all of the same dimensions as E
.
genes
data.frame containing probe information. Should have one row for each probe. May have any number of columns.
targets
data.frame containing information on the target RNA samples. Rows correspond to samples. May have any number of columns.
Valid EList
or EListRaw
objects may contain other optional components, but all probe or sample information should be contained in the above components.
These classes inherit directly from class list
so any operation appropriate for lists will work on objects of this class.
In addition, EList
objects can be subsetted and combined.
EList
objects will return dimensions and hence functions such as dim
, nrow
and ncol
are defined.
EList
s also inherit a show
method from the virtual class LargeDataObject
, which means that ELists
will print in a compact way.
Gordon Smyth
02.Classes gives an overview of all the classes defined by this package.
ExpressionSet
is a more formal class in the Biobase package used for the same purpose.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # Two ways to make an EList object:
y <- matrix(rnorm(10,5),10,5)
rownames(y) <- paste0("Gene",1:10)
colnames(y) <- LETTERS[1:5]
Genes <- data.frame(Chr=sample(1:21,10))
row.names(Genes) <- row.names(y)
# Create the object, than add components:
E <- new("EList")
E$E <- y
E$genes <- Genes
# Create with components:
E <- new("EList", list(E=y, genes=Genes))
|
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