intraModularStatistics: IntraModular Statistics
In Sage-Bionetworks/SageBionetworksCoex: Gene Coexpression

Description Usage Arguments Value Author(s) References

Computes gene-wise connectivity statistics, within and between modules.

1	intraModularStatistics(dichotCor, tomDist, modules)

`dichotCor`	\|cc\|^beta, as computed by clusterGenes()
`tomDist`	Topological Overlap Matrix (TOM) expressed as a distance matrix, as computed by clusterGenes()
`modules`	The module membership of each gene, as computed by modulesFromGeneTree()

Returns a data frame with one row per gene and the following columns: k.in – in-module number of connections of each gene k.in.normed – in-module number of connections of each gene, divided by module size to.in – sum of topological overlaps within modules to.in.normed – sum of topological overlaps within modules, divided by module size k.all – gene connectivity statistic, k. k.all.normed – gene connectivity, k, divided by number of genes. to.all – sum of topological overlaps to.all.normed – sum of topological overlaps, divided by number of genes. k.out – gene connectivity statistic, k, minus in-module number of connections of each gene k.diff – k.in minus k.out to.out – to.all minus to.in to.dif – to.in minus to.out cc.in – within-module cluster coefficient for each gene

Bin Zhang

Zhang, B. & Horvath, S. (2005) Statistical Applications in Genetics and Molecular Biology 4, Article 17.

Sage-Bionetworks/SageBionetworksCoex documentation built on May 9, 2019, 12:11 p.m.