stackDatabases: Combine edges from databases into a data.table

In netgsa: Network-Based Gene Set Analysis

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

netgsa documentation built on Nov. 14, 2023, 5:09 p.m.