checkUserEdges: Check user edgelist for errors
In drjingma/netgsa: Network-Based Gene Set Analysis

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

Read in user edgelist as data.table and check the column formatting and check for conflicting information. This is a helper function in prepareAdjMat and should not be called by the user.

1	checkUserEdges(edgelist, non_edges)

`edgelist`	File path to user specified edgelist. Read in with `data.table::fread`
`non_edges`	File path to user specified non-edgelist. Read in with `data.table::fread`

This function checks to make sure there is the correct number of columns specified in the edgeslist (4 or 5). It also checks for non-numeric values and to see if there is inconsistent information such as an edge specified in the non-edgelist and the edgelist.

A list with components

`user_edges`	A data.table of the user specified edges
`user_non_edges`	A data.table of the user specified non-edges

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.