Gene Relevance methods {destiny} | R Documentation

## 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)

[Package destiny version 3.1.0 Index]