Select a subset of genes stored in the input ExpressionSet.
SelectGeneSet(ExpressionSet, gene.set, use.only.map = FALSE)a standard PhyloExpressionSet or DivergenceExpressionSet object.
a character vector storing the gene ids for which gene expression profiles shall be visualized.
a logical value indicating whether instead of a standard ExpressionSet only a Phylostratigraphic Map or Divergene Map is passed to the function.
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.
data(PhyloExpressionSetExample)
# receive a subset ExpressionSet for the fist 5 genes stored in
# the PhyloExpressionSetExample
SelectGeneSet(ExpressionSet = PhyloExpressionSetExample,
gene.set = PhyloExpressionSetExample[1:5, 2])
#> Phylostratum GeneID Zygote Quadrant Globular Heart Torpedo
#> 1 1 at1g01040.2 2173.635 1911.2001 1152.555 1291.4224 1000.253
#> 2 1 at1g01050.1 1501.014 1817.3086 1665.309 1564.7612 1496.321
#> 3 1 at1g01070.1 1212.793 1233.0023 939.200 929.6195 864.218
#> 4 1 at1g01080.2 1016.920 936.3837 1181.338 1329.4734 1392.643
#> 5 1 at1g01090.1 11424.567 16778.1685 34366.649 39775.6405 56231.569
#> Bent Mature
#> 1 962.9772 1696.4274
#> 2 1114.6435 1071.6555
#> 3 877.2060 894.8189
#> 4 1287.9746 861.2605
#> 5 66980.3673 7772.5617
# 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)
#> Phylostratum GeneID
#> 1 1 at1g01040.2
#> 2 1 at1g01050.1
#> 3 1 at1g01070.1
#> 4 1 at1g01080.2
#> 5 1 at1g01090.1