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Integrate Expression Data with PPI Network

Source: R/DoIntegPPI.R
DoIntegPPI.Rd

Finds common genes between expression data and PPI network, then extracts the maximally connected subnetwork.

Usage

DoIntegPPI(exp.m, ppiA.m)

Arguments

exp.m

Gene expression matrix (genes x cells). Should be library-size normalized. Raw counts will be log2-transformed automatically.

ppiA.m

PPI network adjacency matrix (genes x genes).

Value

List with elements:

expMC

Expression matrix for genes in the maximal component.

adjMC

Adjacency matrix of the maximal connected component.

Details

The function:

  1. Identifies genes present in both expression data and PPI network

  2. Extracts the induced subnetwork

  3. Finds the largest connected component

  4. Returns matched expression and adjacency matrices

References

Teschendorff AE, Enver T. Nat Commun. 2017;8:15599.

Author

Andrew E Teschendorff, Zaoqu Liu

Examples

if (FALSE) { # \dontrun{
data(net13Jun12.m)
exp <- matrix(rpois(5000 * 100, 5), nrow = 5000)
rownames(exp) <- head(rownames(net13Jun12.m), 5000)
integ <- DoIntegPPI(exp, net13Jun12.m)
} # }