featurePairwiseDistances in an SCESet object

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Description

SCESet objects can contain a matrix of pairwise distances between features (e.g. genes, transcripts). These functions conveniently access and replace the gene pairwise distances with the value supplied, which must be a matrix of the correct size. The function featDist is simply shorthand for featurePairwiseDistances.

Usage

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featurePairwiseDistances(object)

featurePairwiseDistances(object) <- value

featDist(object)

featDist(object) <- value

featurePairwiseDistancesSCESet(object)

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

featDistSCESet(object)

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

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

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

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

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

Arguments

object

a SCESet object.

value

a matrix of class "numeric" containing feature pairwise distances

Value

An SCESet object containing new feature pairwise distances matrix.

Author(s)

Davis McCarthy

Examples

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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)
featurePairwiseDistances(example_sceset)

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