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

1 2 3 4 5 6 7 8 9 | ```
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)
``` |

`adjMat` |
adjacency matrix, a square, symmetric matrix with entries between 0 and 1. |

`colors` |
module labels. A vector of length |

`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 |

`distFnc` |
character string specifying the function to be used to calculate co-expression
similarity for distance networks. Defaults to the function |

`distOptions` |
character string specifying additional arguments to be passed to the function given
by |

`networkType` |
network type. Allowed values are (unique abbreviations of) |

`power` |
soft thresholding power. |

`ignoreColors` |
level(s) of |

`getWholeNetworkConnectivity` |
logical: should whole-network connectivity be computed as well? For large networks, this can be quite time-consuming. |

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.

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,

Steve Horvath and Peter Langfelder

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

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