netEstClusts: Estimates network for each cluster
In drjingma/netgsa: Network-Based Gene Set Analysis

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

Estimates network using netEst.dir or netEst.undir for each cluster. This is a helper function in prepareAdjMat and should not be called by the user.

1	netEstClusts(grp, X, group, net_info, n, lambda_c, eta, net_clusters, penalize_diag)

`grp`	Specific group to analyze e.g. condition 1, 2, etc. Same type as `group`
`X`	p x n data matrix
`group`	Vector specifying which columns in the data matrix correspond to which condition or group
`net_info`	List with named elements "zero" and "one" corresponding to the zero and one information matrices used in `netEst.dir` and `netEst.undir`
`n`	Vector of the total number of observations for `grp`. Used to determine `lambda` in `netEst.dir` and `netEst.undir`
`lambda_c`	lambda constant. Used to determine `lambda` in `netEst.dir` and `netEst.undir`
`eta`	Value of eta passed to `netEst.undir`
`net_clusters`	Named numeric vector specifying which genes correspond to which clusters. Names are genes and the values are their corresponding clusters
`penalize_diag`	TRUE/FALSE - whether or not to penalize diagonal

This function loops through each cluster and calls netEst.undir or netEst.dir with the relevant parameters.

A list with components

`Adj`	List of the weighted adjacency matrices (partial correlations) for each cluster. The structure is Adj[[cluster]]. If cluster = FALSE, Adj[[cluster]] only has one element. Note this is used in a lapply where we loop over the groups giving us the final Adj[[condition]][[cluster]] structure.
`invcov`	List of estimated inverse covariance matrices for each cluster. The structure is invcov[[cluster]]. If cluster = FALSE, invcov[[cluster]] only has one element
`lambda`	List of values of tuning parameters used for each cluster.

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.