Usage
intramodularConnectivity(adjMat, colors, scaleByMax = FALSE)
intramodularConnectivity.fromExpr(datExpr, colors,
corFnc = "cor", corOptions = "use = 'p'",
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 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.
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 spec 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.