stackDatabases function

Combine edges from databases into a data.table

Retrieves edges from specified databases and stacks them into one data.table.This is a helper function in prepareAdjMat and should not be called by the user.

stackDatabases(databases)

Arguments

• databases: Character vector of databases to compile. Should be one of the options from hspaiens in graphite::pathwayDatabases()

Details

This function compiles all the edges from all databases specified into one data.table

Returns

A data.table with columns: - database: Which database the edge comes from

• src: Source gene

• src_type: Source gene identifier type

• dest: Destination gene

• dest_type: Destination gene identifier type

• direction: Direction of edge. Either Directed or Undirected

References

Ma, J., Shojaie, A. & Michailidis, G. (2016) Network-based pathway enrichment analysis with incomplete network information. Bioinformatics 32(20):165--3174.

Author(s)

Michael Hellstern

See Also

obtainEdgeList