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])
#>   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