stackDatabases: Combine edges from databases into a data.table
In drjingma/netgsa: Network-Based Gene Set Analysis

Description Usage Arguments Details Value Author(s) References See Also

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.

1	stackDatabases(databases)

databases

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

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

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

Michael Hellstern

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

obtainEdgeList

drjingma/netgsa documentation built on Feb. 22, 2022, 5:18 p.m.