netgsa: Network-Based Gene Set Analysis

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

Convert edgelist and list of non-edges to zero/one matrices used in netEst.dir and netEst.undir. This is a helper function in prepareAdjMat and should not be called by the user.

1	convertEdgeListToZeroOne(edgelist, non_edges, genes, genes_not_in_dbs)

`edgelist`	Data.table of all edges (user specified and those found in graphite)
`non_edges`	Data.table of all non-edges. Graphite doesn't give non-edges so this should only be user specified
`genes`	Character vector of genes
`genes_not_in_dbs`	Character vector of genes not found in the graphite databases

This function converts edges and non-edges into both the zero and one matrices used in netEst.dir and netEst.undir. If two genes are in the graphite databases, but we don't see an edge between them they are classified as having a non-edge. However, if they are not in the graphite database we classify them as having neither an edge between them nor a non-edge between them. We are essentially assuming we have no information on these. The entries in both the zero and one matrices will be 0.

A list with components

`ones_freq`	A pxp matrix with the number of graphite databases a specific edge occurs in as the value
`ones`	A pxp matrix. Values are 1 if the edge occurs at least once, 0 otherwise
`zeros`	A pxp matrix. Values are 1 if we know this is not an edge, 0 otherwise
`directed`	Logical indicating if our edgelist is a directed acyclic graph (DAG). Checked using `igraph::is_dag`

Michael Hellstern

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

prepareAdjMat

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