Select a Subset of Genes in an ExpressionSet

Select a subset of genes stored in the input ExpressionSet.

Usage

SelectGeneSet(ExpressionSet, gene.set, use.only.map = FALSE)

Arguments

ExpressionSet: a standard PhyloExpressionSet or DivergenceExpressionSet object.
gene.set: a character vector storing the gene ids for which gene expression profiles shall be visualized.
use.only.map: a logical value indicating whether instead of a standard ExpressionSet only a Phylostratigraphic Map or Divergene Map is passed to the function.

Details

This function selects a subset of genes specified in gene.set stored in the input ExpressionSet and returns a subset ExpressionSet.

This function is useful for studying the evolutionary properties of a subset of genes stored in the ExpressionSet.

Author

Hajk-Georg Drost

Examples

data(PhyloExpressionSetExample)

# receive a subset ExpressionSet for the fist 5 genes stored in
# the PhyloExpressionSetExample
SelectGeneSet(ExpressionSet = PhyloExpressionSetExample,
            gene.set      = PhyloExpressionSetExample[1:5, 2])
#> Error in PlotGeneSet(ExpressionSet = ExpressionSet, gene.set = gene.set,     get.subset = TRUE, use.only.map = use.only.map): could not find function "PlotGeneSet"
            
            
# get a gene subset using only a phylostratihraphic map
ExamplePSMap <- PhyloExpressionSetExample[ , 1:2]

SelectGeneSet(ExpressionSet = ExamplePSMap,
              gene.set      = PhyloExpressionSetExample[1:5, 2],
              use.only.map  = TRUE)          
#> Error in PlotGeneSet(ExpressionSet = ExpressionSet, gene.set = gene.set,     get.subset = TRUE, use.only.map = use.only.map): could not find function "PlotGeneSet"