ClusterExperiment-methods {clusterExperiment} | R Documentation |
This is a collection of helper methods for the ClusterExperiment class.
## S4 method for signature 'ClusterExperiment' show(object) ## S4 method for signature 'ClusterExperiment' transformation(x) ## S4 replacement method for signature 'ClusterExperiment,'function'' transformation(object) <- value ## S4 method for signature 'ClusterExperiment' nClusterings(x) ## S4 method for signature 'ClusterExperiment' nClusters(x, ignoreUnassigned = TRUE) ## S4 method for signature 'ClusterExperiment' nFeatures(x) ## S4 method for signature 'ClusterExperiment' nSamples(x) ## S4 method for signature 'ClusterExperiment' clusterMatrixNamed(x, whichClusters = "all") ## S4 method for signature 'ClusterExperiment' clusterMatrixColors(x, whichClusters) ## S4 method for signature 'ClusterExperiment,missing' clusterMatrix(x, whichClusters) ## S4 method for signature 'ClusterExperiment,numeric' clusterMatrix(x, whichClusters) ## S4 method for signature 'ClusterExperiment,character' clusterMatrix(x, whichClusters) ## S4 method for signature 'ClusterExperiment' primaryCluster(x) ## S4 method for signature 'ClusterExperiment' primaryClusterIndex(x) ## S4 method for signature 'ClusterExperiment' primaryClusterLabel(x) ## S4 method for signature 'ClusterExperiment' primaryClusterNamed(x) ## S4 method for signature 'ClusterExperiment' primaryClusterType(x) ## S4 method for signature 'ClusterExperiment' subsetByCluster(x, clusterValue, whichCluster = "primary", matchTo = c("name", "clusterIds")) ## S4 replacement method for signature 'ClusterExperiment,numeric' primaryClusterIndex(object) <- value ## S4 method for signature 'ClusterExperiment' dendroClusterIndex(x) ## S4 method for signature 'ClusterExperiment' coClustering(x) ## S4 replacement method for signature 'ClusterExperiment,matrix' coClustering(object) <- value ## S4 method for signature 'ClusterExperiment' clusterTypes(x) ## S4 method for signature 'ClusterExperiment' clusteringInfo(x) ## S4 method for signature 'ClusterExperiment' clusterLabels(x) ## S4 replacement method for signature 'ClusterExperiment,character' clusterLabels(object) <- value ## S4 method for signature 'ClusterExperiment' clusterLegend(x) ## S4 replacement method for signature 'ClusterExperiment,list' clusterLegend(object) <- value ## S4 method for signature 'ClusterExperiment,character' renameClusters(object, value, whichCluster = "primary", matchTo = c("name", "clusterIds")) ## S4 method for signature 'ClusterExperiment,character' recolorClusters(object, value, whichCluster = "primary", matchTo = c("name", "clusterIds")) ## S4 method for signature 'ClusterExperiment' orderSamples(x) ## S4 replacement method for signature 'ClusterExperiment,numeric' orderSamples(object) <- value ## S4 replacement method for signature 'ClusterExperiment,character' clusterTypes(object) <- value ## S4 method for signature 'ClusterExperiment' addToColData(object, ...) ## S4 method for signature 'ClusterExperiment' colDataClusters(object, whichClusters = "primary", useNames = TRUE, makeFactor = TRUE, ...)
x, object |
a ClusterExperiment object. |
value |
The value to be substituted in the corresponding slot. See the
slot descriptions in |
ignoreUnassigned |
logical. If true, ignore the clusters with -1 or -2 assignments in calculating the number of clusters per clustering. |
whichClusters |
argument that can be either numeric or character value
indicating the clusters to be used. If numeric, gives the indices of the
|
clusterValue |
values of the cluster to match to for subsetting |
whichCluster |
argument to identify cluster, taking input like
|
matchTo |
for subsetting, whether to match to the cluster name
( |
... |
For |
useNames |
for |
makeFactor |
logical for |
Note that redefining the transformation function via
transformation(x)<-
will check the validity of the transformation on
the data assay. If the assay is large, this may be time consuming. Consider
using a call to ClusterExperiment, which has the option as to whether to
check the validity of the transformation.
transformation
prints the function used to transform the data
prior to clustering.
nClusterings
returns the number of clusterings (i.e., ncol of
clusterMatrix).
nClusters
returns the number of clusters per clustering
nFeatures
returns the number of features (same as 'nrow').
nSamples
returns the number of samples (same as 'ncol').
clusterMatrixNamed
returns a matrix with cluster labels.
clusterMatrixColors
returns the matrix with all the clusterings, using the internally stored colors for each cluster
clusterMatrix
returns the matrix with all the clusterings.
clusterMatrix
returns the matrix with all the clusterings.
clusterMatrix
returns the matrix with all the clusterings.
primaryCluster
returns the primary clustering (as numeric).
primaryClusterIndex
returns/sets the primary clustering index
(i.e., which column of clusterMatrix corresponds to the primary clustering).
primaryClusterIndex
returns/sets the primary clustering index
(i.e., which column of clusterMatrix corresponds to the primary clustering).
primaryClusterNamed
returns the primary cluster (using cluster
labels).
primaryClusterIndex
returns/sets the primary clustering index
(i.e., which column of clusterMatrix corresponds to the primary clustering).
subsetByCluster
subsets the object by clusters in a clustering
and returns a ClusterExperiment object with only those samples
dendroClusterIndex
returns/sets the clustering index
of the clusters used to create dendrogram
(i.e., which column of clusterMatrix corresponds to the clustering).
coClustering
returns/sets the co-clustering matrix.
clusterTypes
returns/sets the clusterTypes slot.
clusteringInfo
returns the clusterInfo slot.
clusterLabels
returns/sets the column names of the clusterMatrix slot.
clusterLegend
returns/sets the clusterLegend slot.
renameClusters
changes the names assigned to clusters within a clustering
recolorClusters
changes the colors assigned to clusters within a clustering
orderSamples
returns/sets the orderSamples slot.
addToColData
returns a ClusterExperiment
object
with the clusterings in clusterMatrix slot added to the colData
slot
colDataClusters
returns a DataFrame
object
that has the clusterings in clusterMatrix slot added to the
DataFrame
in the colData
slot