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.

# S4 method for GeneRelevance
print(x)

# S4 method for GeneRelevance
show(object)

# S4 method for GeneRelevance
featureNames(object)


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

# S4 method for GeneRelevance
dataset(object)

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

# S4 method for GeneRelevance
distance(object)

# S4 method for 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

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)