Helper methods for the ClusterExperiment class

Share:

Description

This is a collection of helper methods for the ClusterExperiment class.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
## S4 method for signature 'ClusterExperiment,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'ClusterExperiment'
show(object)

## S4 method for signature 'ClusterExperiment'
clusterMatrixNamed(x)

## S4 method for signature 'ClusterExperiment'
primaryClusterNamed(x)

## S4 method for signature 'ClusterExperiment'
transformation(x)

## S4 method for signature 'ClusterExperiment'
nClusters(x)

## S4 method for signature 'ClusterExperiment'
nFeatures(x)

## S4 method for signature 'ClusterExperiment'
nSamples(x)

## S4 method for signature 'ClusterExperiment'
clusterMatrix(x)

## S4 method for signature 'ClusterExperiment'
primaryCluster(x)

## S4 method for signature 'ClusterExperiment'
primaryClusterIndex(x)

## S4 replacement method for signature 'ClusterExperiment,numeric'
primaryClusterIndex(object) <- value

## 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'
clusterInfo(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'
orderSamples(x)

## S4 replacement method for signature 'ClusterExperiment,numeric'
orderSamples(object) <- value

## S4 replacement method for signature 'ClusterExperiment,character'
clusterTypes(object) <- value

Arguments

x, object

a ClusterExperiment object.

..., i, j, drop

Forwarded to the SummarizedExperiment method.

value

The value to be substituted in the corresponding slot. See the slot descriptions in ClusterExperiment for details on what objects may be passed to these functions.

Details

Note that when subsetting the data, the dendrogram information and the co-clustering matrix are lost.

Value

clusterMatrixNamed returns a matrix with cluster labels.

primaryClusterNamed returns the primary cluster (using cluster labels).

transformation prints the function used to transform the data prior to clustering.

nClusters returns the number of clusterings (i.e., ncol of clusterMatrix).

nFeatures returns the number of features (same as 'nrow').

nSamples returns the number of samples (same as 'ncol').

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).

coClustering returns/sets the co-clustering matrix.

clusterTypes returns/sets the clusterTypes slot.

clusterInfo returns the clusterInfo slot.

clusterLabels returns/sets the column names of the clusterMatrix slot.

clusterLegend returns/sets the clusterLegend slot.

orderSamples returns/sets the orderSamples slot.