cellPairwiseDistances in an SCESet object

Share:

Description

SCESet objects can contain a matrix of pairwise distances between cells. These functions conveniently access and replace the cell pairwise distances with the value supplied, which must be a matrix of the correct size. The function cellDist is simply shorthand for cellPairwiseDistances.

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
cellPairwiseDistances(object)

cellPairwiseDistances(object) <- value

cellDist(object)

cellDist(object) <- value

cellPairwiseDistances.SCESet(object)

## S4 method for signature 'SCESet'
cellPairwiseDistances(object)

cellDistSCESet(object)

## S4 method for signature 'SCESet'
cellDist(object)

## S4 replacement method for signature 'SCESet,matrix'
cellPairwiseDistances(object) <- value

## S4 replacement method for signature 'SCESet,dist'
cellPairwiseDistances(object) <- value

## S4 replacement method for signature 'SCESet,matrix'
cellDist(object) <- value

## S4 replacement method for signature 'SCESet,dist'
cellDist(object) <- value

Arguments

object

a SCESet object.

value

a matrix of class "numeric" containing cell pairwise distances

Value

An SCESet object containing new cell pairwise distances matrix.

Author(s)

Davis McCarthy

Examples

1
2
3
4
5
data("sc_example_counts")
data("sc_example_cell_info")
pd <- new("AnnotatedDataFrame", data = sc_example_cell_info)
example_sceset <- newSCESet(countData = sc_example_counts, phenoData = pd)
cellPairwiseDistances(example_sceset)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.