This is the main class used to store sets of marker
genes, for use in gene expression deconvolution methods.
It serves as a light version of class
MarkerSetCollection-class
, assuming that
all marker identifiers are of the same type (e.g., entrez
gene, unigene or probe ids), and are relative to the same
platform, organism, etc.. (see details).
isMarkerList
tests if an object is a
MarkerList-class
object.
attachMarkers
attaches a marker list to an
NMF
object, by storing it in an attribute named
'markers'
. It actually stores the results from
MarkerList(x)
, that is a MarkerList
object.
getMarkers
extracts the marker list from the
attribute named 'markers'
that will generally
contain a MarkerList
object.
has.markers
tells if an object has an attached
marker list, i.e. an attribute named 'markers'
.
isMarkerList(x)
S4 (MarkerList)
`summary`(object)
attachMarkers(x, object)
getMarkers(x, err.notfind = NULL, unlist = FALSE)
has.markers(x)
MarkerList
object or any
object depending on the method. See their respective
description for details.MarkerList
object, or any object with an attached
list of markers (cf. attachMarkers
and
getMarkers
), depending on the method. See their
respective description for details.x
has no marker list attached.
The error is only thrown if err.notfind
is not
NULL
.FALSE
.summary returns a numeric vector containing the number of markers for each cell-type
attachMarkers
returns object
with an
attribute named 'markers'
that contains the result
of MarkerList(x)
.
getMarkers
returns the attached marker
list
has.markers
returns a logical
The objective of the MarkerList
class is to
simplify the structure and processing of gene lists,
compared to handling MarkerSetCollection
objects.
Conversion methods between these two classes are
provided.
The class is essentially a named list, in which each element contains data about a set of marker features/genes, e.g., from a given cell-type. Marker features are assumed to be exclusive to each set, i.e. they appear in only one element of the list. In addition to their identifiers, markers can be associated with numeric values, e.g., corresponding to p-values or specificity scores, or integer, which are then interpreted as indexes relative to some expression data.
It contains the same slots as
GeneSet-class
, which are used when
converting MarkerList
objects into
MarkerSetCollection
objects, to fill the slots of
all gene set. For a description of each slot, please see
the documentation for GeneSet-class
.
signature(x = "MarkerList", i = "ANY", j =
"ANY")
: MarkerList
objects have convenient subset
methods, that allow to subset the list not only along the
sets (first dimension) but also along the markers, which
proves to be very useful to subset markers list based on
another set of identifier, e.g., the genes present in
some expression data, or in another marker list.
The method `[`
works performs basic strict subsets
using integer, character and logical subsetting vectors.
See [,MarkerList,ANY,ANY-method
for more
details.
signature(x = "MarkerList", i = "list", j
= "ANY")
: This method subsets/reorders each set of
marker using a subset specification found in
signature(x = "MarkerList", i = "missing",
j = "list")
: This method is equivalent to x[i, ,
..., match.names=FALSE]
, i.e. that each element of the
marker list x
are subset/reordered as its
corresponding one in j
, following the lists' order
-- with no attempt to match their elements names before
subsetting.
signature(object =
"MarkerList")
: Extract name of the annotation package
from a marker list.
signature(object =
"MarkerList", value = "character")
: Sets the name of the
annotation package associated to a marker list.
signature(object =
"MarkerList", value = "NULL")
: Reset the annotation
package associated to a marker list
signature(object = "MarkerList")
:
This method combines markers of cell types that belong to
the same CBC group.
signature(object = "MarkerList")
:
This method allows to add annotation tracks in heatmaps
produced by aheatmap
, to highlight the
position of markers, when plotting either the global
expression values or cell type-specific signatures,
whether measured or estimated.
signature(x = "MarkerList", y =
"factor")
: Combine markers from multiple cell types of a
MarkerList object, based on groups defined by a given
factor.
signature(e1 = "MarkerList", e2 =
"numeric")
: Compare
compares all embedded values
with a given fixed value. This is useful to filter
markers based on their associated scores.
signature(object =
"MarkerList")
: Computes the connectivity matrix of each
set (i.e. cell/tissue type) of a marker list, i.e. the
matrix whose entries are the number of features in common
between each pair o cell type.
signature(object = "MarkerList",
to = "GeneIdentifierType", from = "GeneIdentifierType")
:
Convert IDs from a MarkerList object.
In this case, argument unlist
indicates if the
result should be a simple list containing the mapping (a
list) for each cell type or a
MarkerList-class
object (default).
signature(object = "MarkerList")
:
Shows more details than the regular show
method.
signature(x = "MarkerList")
:
drop
drops empty sets of markers from a
MarkerList
object, as well as markers with
FALSE
values if the object is a logical marker
list. It returns the reduced MarkerList
object.
signature(object =
"MarkerList")
: Returns the character vector of all
marker names in the list.
signature(object = "MarkerList")
:
For MarkerList
objects the conversion is
similar to what unlist
would do, but
argument use.names
is used slightly differently.
Secondly, the names of the main elements are append to
the marker names (like unlist
does if
use.names=TRUE
) only for marker lists that contain
numeric values (e.g. specificity scores). In the other
cases, they are used either as values for character
marker lists or as duplicated names for integer marker
lists.
signature(object =
"MarkerList")
: Returns the type of gene identifier used
in a marker list.
signature(object =
"MarkerList", value = "NULL")
: Sets the type of gene
identifier used in a marker list to
NullIdentifier()
.
signature(object =
"MarkerList", value = "character")
: Sets the type of
gene identifier used in a marker list to a given value.
signature(object =
"MarkerList", value = "GeneIdentifierType")
: Sets the
type of gene identifier associated with a marker list to
a given GeneIdentifierType-class
object.
signature(object =
"MarkerList")
: Returns the values embedded in a
MarkerList
object.
signature(x = "MarkerList")
:
Computes the incidence matrix of each feature in each set
(i.e. cell/tissue type) of a marker list.
The matrix is computed by converting the
MarkerList
object into a
GeneSetCollection
object, for which a
method incidence
exists in the
GSEABase package.
signature(object =
"MarkerList")
: This method acts as a Constructor-Copy
that returns the input MarkerList object unchanged if no
other argument are passed, or creates a new MarkerList
object based on object
, using the arguments in
...
to initialise the slots.
signature(object = "MarkerList",
data = "matrix")
: Workhorse method is for
markermap
.
signature(object = "MarkerList",
data = "ExpressionSet")
: The method markermap
for
ExpressionSet
objects calls the main
markermap
method on the expression matrix
exprs(object)
.
signature(object = "MarkerList",
data = "NMF")
: The method markermap
for
NMF
objects calls the main markermap
method
on the basis matrix basis(object)
.
signature(object = "MarkerList",
data = "NMFfitX")
: The method markermap
for
NMFfitX
objects calls the main markermap
method on the best fit fit(object)
.
signature(x = "MarkerList")
: The
method reorder
for MarkerList
objects
allows to reorder each set of markers according to some
auxiliary reference data, e.g, their gene expression in
different cell types.
See reorder,MarkerList-method
for more
details.
signature(X = "MarkerList")
: Applies
a given function to a MarkerList-class
object.
signature(x = "MarkerList")
:
subset
subset a MarkerList
object keeping
only the markers that are present with a given reference
set, which can be a character vector, the rownames of a
matrix or an NMF
object, or the feature names of
an ExpressionSet
. The markers are matched using
the function matchIndex
, and gene identifier
conversion is performed if necessary.
signature(object = "MarkerList")
:
Summary method for MarkerList
objects
signature(object = "MarkerList")
:
Summary method for MarkerList
objects
Due to the structure of MarkerList
objects, all
gene identifiers must share the same set of
characteristics. However, it is possible to associate a
MarkerList
object with multiple annotation
packages, which will be correctly dealt with if all the
list's identifiers are found in only one of them. For
example the registered maker list Abbas is
associated with annotation packages hgu133a.db
and
hgu133b.db
.