intramodularConnectivity: Calculation of intramodular connectivity

In WGCNA: Weighted Correlation Network Analysis

Calculation of intramodular connectivity

Description

Calculates intramodular connectivity, i.e., connectivity of nodes to other nodes within the same module.

Usage

intramodularConnectivity(adjMat, colors, scaleByMax = FALSE)

intramodularConnectivity.fromExpr(datExpr, colors, 
              corFnc = "cor", corOptions = "use = 'p'",
              weights = NULL,
              distFnc = "dist", distOptions = "method = 'euclidean'",
              networkType = "unsigned", power = if (networkType=="distance") 1 else 6,
              scaleByMax = FALSE,
              ignoreColors = if (is.numeric(colors)) 0 else "grey",
              getWholeNetworkConnectivity = TRUE)

Arguments

adjMat	adjacency matrix, a square, symmetric matrix with entries between 0 and 1.
colors	module labels. A vector of length ncol(adjMat) giving a module label for each gene (node) of the network.
scaleByMax	logical: should intramodular connectivities be scaled by the maximum IM connectivity in each module?
datExpr	data frame or matrix containing expression data. Columns correspond to genes and rows to samples.
corFnc	character string specifying the function to be used to calculate co-expression similarity for correlation networks. Defaults to Pearson correlation. Any function returning values between -1 and 1 can be used.
corOptions	character string specifying additional arguments to be passed to the function given by corFnc. Use "use = 'p', method = 'spearman'" to obtain Spearman correlation.
weights	optional matrix of the same dimensions as datExpr, giving the weights for individual observations in datExpr. These will be passed on to the correlation function.
distFnc	character string specifying the function to be used to calculate co-expression similarity for distance networks. Defaults to the function dist. Any function returning non-negative values can be used.
distOptions	character string specifying additional arguments to be passed to the function given by distFnc. For example, when the function dist is used, the argument method can be used to specify various ways of computing the distance.
networkType	network type. Allowed values are (unique abbreviations of) "unsigned", "signed", "signed hybrid", "distance".
power	soft thresholding power.
ignoreColors	level(s) of colors that identifies unassigned genes. The intramodular connectivity in this "module" will not be calculated.
getWholeNetworkConnectivity	logical: should whole-network connectivity be computed as well? For large networks, this can be quite time-consuming.

Details

The module labels can be numeric or character. For each node (gene), the function sums adjacency entries (excluding the diagonal) to other nodes within the same module. Optionally, the connectivities can be scaled by the maximum connectivy in each module.

Value

If input getWholeNetworkConnectivity is TRUE, a data frame with 4 columns giving the total connectivity, intramodular connectivity, extra-modular connectivity, and the difference of the intra- and extra-modular connectivities for all genes; otherwise a vector of intramodular connectivities,

Author(s)

Steve Horvath and Peter Langfelder

References

Dong J, Horvath S (2007) Understanding Network Concepts in Modules, BMC Systems Biology 2007, 1:24

See Also

adjacency

WGCNA documentation built on Sept. 18, 2024, 5:08 p.m.