mirsynergy {Mirsynergy} | R Documentation |
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.
mirsynergy(W, H, alpha = 2, merge.tol = 0.8, density1.tol = 1e-2, density2.tol=5e-3, verbose = FALSE)
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. |
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.
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 |
Yue Li
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
##---- 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)