cellPairwiseDistances: cellPairwiseDistances in an SCESet object

In dynverse/scaterlegacy: Single-cell analysis toolkit for gene expression data in R

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

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

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)

dynverse/scaterlegacy documentation built on Feb. 17, 2020, 5:07 a.m.