infer.edge.type {nem}R Documentation

Infer regulation direction for each edge

Description

The method infers edge types (up-regulation, down-regulation) for a given nem model. For an edge a->b the method looks at the fraction of E-genes attached to b (including b itself), which are up- or down-regulated in a knock-down of a. If significantly more genes are down-regulated than up-regulated, the edge a->b is assumed to be an activation. Likewise, if significantly more genes are up-regulated than down-regulated, a->b is assumed to be an inhibition. If there is no significant difference in up- and down-regulated edges, a->b does not have a specified type.

Usage

infer.edge.type(x, logFC, alpha=0.05, adj.method="BY")

Arguments

x nem object
logFC matrix with fold changes. The rownames of this matrix should correspond to the rownames of the data matrix, which was used to infer the nem model.
alpha p-value cutoff
adj.method multiple testing correction method. Default: Benjamini-Yekutieli

Details

Significance is calculated using a two-tailed binomial test with null hypothesis p=0.5.

Value

Modified nem object. Each edge in the nem graph now has a "weight" and a "label" attribute. The label attribute corresponds to the original value in the adjacency matrix. The weight attribute encodes up- and down-regulation in the following way: value 2 means up-regulation, value -1 down-regulation and value 1 corresponds to an unknown regulation type.

Author(s)

Holger Froehlich

See Also

binom.test

Examples

        data("BoutrosRNAi2002") 
        D <- BoutrosRNAiDiscrete[,9:16]
        p <- c(.13,.05)
        result = nem(D, para=p)
        resEdgeInf = infer.edge.type(result, BoutrosRNAiLogFC)
        plot(resEdgeInf)

[Package nem version 2.6.0 Index]