Prepare data for gsHistogram(). — buildHistogramData • GeDi

Prepare the data for the gsHistogram() by generating a data.frame which maps geneset names / identifiers to the size of their size.

buildHistogramData(genesets, gs_names, start = 0, end = 0)

Arguments

genesets: a list, A list of genesets where each genesets is represented by list of genes.
gs_names: character vector, Name / identifier of the genesets in genesets
start: numeric, Optional, describes the minimum gene set size to include. Defaults to 0.
end: numeric, Optional, describes the maximum gene set size to include. Defaults to 0.

Value

A data.frame mapping geneset names to sizes

Examples

## Mock example showing how the data should look like
gs_names <- c("a", "b", "c", "d", "e", "f", "g", "h", "i")
genesets <- list(
  c("PDHB", "VARS2"), c("IARS2", "PDHA1"),
  c("AAAS", "ABCE1"), c("ABI1", "AAR2"), c("AATF", "AMFR"),
  c("BMS1", "DAP3"), c("AURKAIP1", "CHCHD1"), c("IARS2"),
  c("AHI1", "ALMS1")
)

p <- buildHistogramData(genesets, gs_names)

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