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