GeDi main function

GeDi(
  genesets = NULL,
  ppi_df = NULL,
  distance_scores = NULL,
  col_name_genesets = "Genesets",
  col_name_genes = "Genes"
)

Arguments

genesets: a data.frame, The input data used for GeDi. This should be a data.frame of at least two columns.One column should be called "Genesets" and contain some sort of identifiers for the individual genesets. In this application, we use the term "Genesets" to refer to collections of individual genes, which share common biological characteristics or functions. Such genesets can for example be obtained from databases such as the Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, or the Molecular Signatures Database (MSigDB). The identifiers used in these databases can be directly used as geneset identifiers in GeDi. The second column should be called "Genes" and contain a list of genes belonging to the individual genesets in the "Genesets" column. In order to leverage all of the functionality available in GeDi, the column has to contain gene names and no other commonly used identifiers. The column names are case sensitive.
ppi_df: a data.frame, Protein-protein interaction (PPI) network data frame. The object is expected to have three columns, Gene1 and Gene2 which specify the gene names of the interacting proteins in no particular order (symmetric interaction) and a column combined_score which is a numerical value of the strength of the interaction.
distance_scores: A Matrix::Matrix() of (distance) scores
col_name_genesets: character, the name of the column in which the geneset ids are listed. Defaults to "Genesets".
col_name_genes: character, the name of the column in which the genes are listed. Defaults to "Genes".

Value

A Shiny app object is returned

Examples

if (interactive()) {
  GeDi()
}
# Alternatively, you can also start the application with your data directly
# loaded.

data("macrophage_topGO_example", package = "GeDi")
if (interactive()) {
  GeDi(genesets = macrophage_topGO_example)
}