GeneColorSet-class {GSEABase} | R Documentation

## Class "GeneColorSet"

### Description

A `GeneColorSet` extends `GeneSet` to allow genes to be 'colored'. Coloring means that for a particular phenotype, each gene has a color (e.g., expression levels "up", "down", or "unchanged") and a phenotypic consequence (e.g., the phenotype is "enhanced" or "reduced").

All operations on a `GeneSet` can be applied to a `GeneColorSet`; coloring can also be accessed.

### Objects from the Class

Construct a `GeneColorSet` with a `GeneColorSet` method. These methods are identical to those for `GeneSet`, except they require an additional `phenotype` argument to specify the phenotype to which the genetic and phenotypic coloring apply. A `GeneColorSet` can be constructed from a `GeneSet` with `GeneColorSet(<GeneSet>, phenotype="<phenotype>").`

### Slots

A `GeneColorSet` inherits all slots from `GeneSet`, and gains the following slots:

`phenotype`:

  Object of class `"ScalarCharacter"` describing the phenotype for which this gene set is colored.

`geneColor`:

  Object of class `"factor"` describing the coloring of each gene in the set. The lengths of `geneColor` and `gene` must be equal.

`phenotypeColor`:

  Object of class `"factor"` describing the phenotypic coloring of each gene in the set. The lengths of `phenotypeColor` and `gene` must be equal.

### Extends

Class `"GeneSet"`, directly.

### Methods

Methods unique to `GeneColorSet` include:

coloring

  `signature(object = "GeneColorSet")`: retrieve coloring as a `data.frame`. The row names of the data frame are the gene names; the columns are `geneColor` and `phenotypeColor`.

coloring<-

  `signature(object = "GeneColorSet", value = "data.frame")`: use a `data frame` to assign coloring information. The `data.frame` must have the same number of rows as the `GeneColorSet` has genes (though see the examples below for flexible ways to alter coloring of a subset of genes). Row names of the `data.frame` correspond to gene names. The data frame has two columns, named `geneColor` and `phenotypeColor`. These must be of class `factor`.

  A typical use of `coloring<-` is to simultaneous extract, subset, and reassign the current coloring, e.g., `coloring(<GeneColorSet>)[1:5,"geneColor"] <- "up"`; see the examples below.

geneColor<-

  `signature(object = "GeneColorSet", value = "factor")`: assign gene colors.

geneColor

  `signature(object = "GeneColorSet")`: retrieve gene colors as a `factor`.

phenotypeColor<-

  `signature(object = "GeneColorSet", value = "factor")`: assign phenotype colors.

phenotypeColor

  `signature(object = "GeneColorSet")`: retrieve phenotype colors as a `factor`.

phenotype<-

  `signature(object = "GeneColorSet", value = "character")`: assign the phenotype from a single-element character vector.

phenotype

  `signature(object = "GeneColorSet")`: retrieve the phenotype as a single-element `character`.

`GeneColorSet` inherits all methods from class `GeneSet`. Methods with different behavior include

[

  `signature(x = "GeneSet", i="character")` `signature(x = "GeneSet", i="numeric")`: subset the gene set by index (`i="numeric"`) or gene value (`i="character"`). Genes are re-ordered as required. `geneColor` and `phenotypeColor` are subset as appropriate.

[[

  `signature(x = "GeneSet")`: select a single gene from the gene set, returning a named character vector of `gene, geneColor, phenotypeColor`. Exact matches only.

\$

  `signature(x = "GeneSet")`: select a single gene from the gene set, returning a named character vector of `gene, geneColor, phenotypeColor`. Provides partial matching into the list of genes.

mapIdentifiers

  `signature(x="GeneColorSet", to="*", from="*")`: checks that gene- and phenotype colors are consistent for mapped identifiers, e.g., that two `AnnotationIdentifiers` mapping to the same `SymbolIdentifier` are colored the same.

Logical (set) operations `&, |, setdiff` warn if the `phenotype` `geneColor`, or `phenotypeColor` differs between sets; this implies coercion of factor levels, and the consequences should be carefully considered.

### Author(s)

Martin Morgan <Martin.Morgan@RoswellPark.org>

### See Also

`GeneSet`.

### Examples

    ## Create a GeneColorSet from an ExpressionSet
    data(sample.ExpressionSet)
    gcs1 <- GeneColorSet(sample.ExpressionSet[100:109],
                         phenotype="imaginary")
    gcs1
    ## or with color...
    gcs2 <- GeneColorSet(sample.ExpressionSet[100:109],
                         phenotype="imaginary",
                         geneColor=factor(
                           rep(c("up", "down", "unchanged"),
                               length.out=10)),
                         phenotypeColor=factor(
                           rep(c("enhanced", "reduced"),
                               length.out=10)))
    coloring(gcs2)

    ## recode geneColor of genes 1 and 4
    coloring(gcs2)[c(1,4),"geneColor"] <- "down"
    coloring(gcs2)
    ## reset, this time by gene name
    coloring(gcs2)[c("31339_at", "31342_at"),"geneColor"] <- c("up", "up")
    ## usual 'factor' errors and warning apply:
    coloring(gcs2)[c("31339_at", "31342_at"),"geneColor"] <- c("UP", "up")

    gcs2[["31342_at"]]
    try(gcs2[["31342_"]]) # no partial matching
    gcs2$"31342" # 1 partial match ok

[Package GSEABase version 1.54.0 Index]