Split string of genes — getGenes • GeDi

Split a long string of space separated genes into a list of individual genes.

getGenes(genesets, gene_name = NULL)

Arguments

genesets: a data.frame, A data.frame with at least two columns. One should be called Geneset, containing the names/identifiers of the genesets in the data. The second column should be called Genes and contains one string of the genes contained in each geneset.
gene_name: a character, Alternative name for the column containing the genes in genesets. If not given, the column is expected to be called Genes.

Value

A list containing for each geneset in the Geneset column a list of the included genes.

Examples

## Mock example showing how the data should look like
df <- data.frame(
  Geneset = c(
    "Cell Cycle",
    "Biological Process",
    "Mitosis"
  ),
  Genes = c(
    c("PDHB,VARS2,IARS2"),
    c("LARS,LARS2"),
    c("IARS,SUV3")
  )
)
genes <- getGenes(df)

## Example using the data available in the package
data(macrophage_topGO_example_small,
     package = "GeDi",
     envir = environment())
genes <- getGenes(macrophage_topGO_example_small)