select_ntop_per_pwy: Select top drivers for a pathway
In jdreyf/PANTS: Pathway analysis via network smoothing

Description Usage Arguments Details Value

Select ntop top drivers for a pathway by calculating impact, sorting nodes with alternative, and selecting top nodes.

1	select_ntop_per_pwy(zscores, nonz.scores, Gmat, pwy, ker, ntop = 3)

`zscores`	Matrix with rownames as feature names, and 1st column with z-scores to select high impact nodes. Non-`NA` values should be finite.
`nonz.scores`	Matrix with rownames as feature names, and 1st column with scores (not z-scores) to select high impact nodes. Non-`NA` values should be finite.
`Gmat`	Binary feature (e.g. gene) by pathway inclusion matrix, indicating which features are in which pathways.
`pwy`	Pathway, must be a column name of `Gmat`.
`ker`	Laplacian kernel matrix representing the interaction network.
`ntop`	Number of top features that most impact a pathway to include.

Independent of the alternative, pathway significance is most affected by nodes with largest magnitude impact, however these nodes are sorted in the output according to alternative="greater". Nodes outside the pathway with no impact, which may arise when the kernel is diagonal, are removed.

Data frame with ntop rows ordered by impact & 3 columns: node with node names; impact with impact values; in.pwy with logicals if node is in pwy.

jdreyf/PANTS documentation built on July 18, 2019, 10:12 a.m.