mirsynergy {Mirsynergy} | R Documentation

## Detect synergistic miRNA regulatory modules by overlapping neighbourhood expansion

### Description

Detect synergistic miRNA regulatory modules by overlapping neighbourhood expansion using a deterministic overlapping clustering algorithm adapted from a recently developed framework. Mirsynergy operates in two stages that first forms MRM based on co-occurring miRNAs and then expand the MRM by greedily including (excluding) mRNA into (from) the MRM to maximize the synergy score, which is a function of miRNA-mRNA and gene-gene interactions.

### Usage

    mirsynergy(W, H, alpha = 2, merge.tol = 0.8,
      density1.tol = 1e-2, density2.tol=5e-3, verbose = FALSE)

### Arguments

`W` | An N by M edge weight matrix containing interaction strength between N mRNA and M miRNA.
`H` | An N by N edge weight matrix containing the binary interaction among the N mRNA (genes).
`alpha` | Penalty for including a node into the growing module (advanced option). See manuscript or Nepusz et al. (2012) for more details.
`merge.tol` | Threshold with range [0,1] to merge modules based on the percentage of nodes shared between the two modules.
`density1.tol` | Threshold with range [0,1] to filter modules by the density function at stage 1 clustering.
`density2.tol` | Threshold with range [0,1] to filter modules by the density function 2 at stage 2 clustering.
`verbose` | Binary indicator to show running info.

### Details

The weight matrix W can be obtained by various approaches such as Pearson correlation or linear regression on mRNA and miNRA expression profiles across multiple samples. Matrix H can be obtained from public database such as TRANSFAC and BioGrid.

### Value

A nested list containing each item as a miRNA regulatory module (MRM). Each item itself is a list containing the following information:

`miRNA` | miRNA included in the MRM
`mRNA` | mRNA included in the MRM
`v.in` | miRNA and mRNA
`v.bound` | miRNA and mRNA disregard or excluded from the MRM but still have nonzero connection with the internal nodes
`card.m` | Number of miRNA in the MRM
`card.t` | Number of mRNA targets in the MRM
`card` | Total number of miRNA and mRNA targets in the MRM
`density` | Density of the MRM

### Author(s)

Yue Li

### References

Nepusz, T., Yu, H., & Paccanaro, A. (2012). Detecting overlapping protein complexes in protein-protein interaction networks. Nature Methods, 9(5), 471-472. doi:10.1038/nmeth.1938

### Examples

    ##---- Should be DIRECTLY executable !! ----
    ##-- ==>  Define data, use random,
    ##--	or do  help(data=index)  for the standard data sets.
    ##
    # simulate N mRNA and M miRNA and their interaction matrices
    load(system.file("extdata/toy_modules.RData", package="Mirsynergy"))

    # run mirsynergy clustering
    V <- mirsynergy(W, H, verbose=TRUE)

    summary_modules(V)

[Package Mirsynergy version 1.14.1 Index]