Gene-Relevance-methods: Gene Relevance methods

In theislab/destiny: Creates diffusion maps

Gene Relevance methods

Description

featureNames <- ... can be used to set the gene names used for plotting (e.g. if the data contains hardly readably gene or transcript IDs). dataset gets the expressions used for the gene relevance calculations, and distance the distance measure.

Usage

## S4 method for signature 'GeneRelevance'
print(x)

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

## S4 method for signature 'GeneRelevance'
featureNames(object)

## S4 replacement method for signature 'GeneRelevance,characterOrFactor'
featureNames(object) <- value

## S4 method for signature 'GeneRelevance'
dataset(object)

## S4 replacement method for signature 'GeneRelevance'
dataset(object) <- value

## S4 method for signature 'GeneRelevance'
distance(object)

## S4 replacement method for signature 'GeneRelevance'
distance(object) <- value

Arguments

x, object	GeneRelevance object
value	A text vector (character or factor)

Value

dataset, distance, and featureNames return the stored properties. The other methods return a GeneRelevance object (print, ... <- ...), or NULL (show), invisibly

See Also

gene_relevance, Gene Relevance plotting

Examples

data(guo_norm)
dm <- DiffusionMap(guo_norm)
gr <- gene_relevance(dm)
stopifnot(distance(gr) == distance(dm))
featureNames(gr)[[37]] <- 'Id2 (suppresses differentiation)'
# now plot it with the changed gene name(s)

theislab/destiny documentation built on Nov. 19, 2024, 5:43 a.m.