stackDatabases {netgsa}

Combine edges from databases into a data.table

Description

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.

Usage

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

Value

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

Author(s)

Michael Hellstern

References

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

See Also

obtainEdgeList