miRSM {miRSM}R Documentation

miRSM

Description

Identify miRNA sponge modules using cannonical correlation (CC) and sensitivity cannonical correlation (SCC) methods

Usage

miRSM(miRExp, ceRExp, mRExp, miRTarget, CandidateModulegenes,
  typex = "standard", typez = "standard", nperms = 100,
  method = c("CC", "SCC"), num_shared_miRNAs = 3,
  pvalue.cutoff = 0.05, CC.cutoff = 0.8, SCC.cutoff = 0.3)

Arguments

miRExp

A SummarizedExperiment object. miRNA expression data: rows are samples and columns are miRNAs.

ceRExp

A SummarizedExperiment object. ceRNA expression data: rows are samples and columns are ceRNAs.

mRExp

A SummarizedExperiment object. mRNA expression data: rows are samples and columns are mRNAs.

miRTarget

A SummarizedExperiment object. Putative miRNA-target binding information.

CandidateModulegenes

List object: a list of candidate miRNA sponge modules.

typex

The columns of x unordered (type='standard') or ordered (type='ordered').

typez

The columns of z unordered (type='standard') or ordered (type='ordered').

nperms

The number of permutations.

method

The method selected to identify miRNA sponge modules, including 'CC' and 'SCC'.

num_shared_miRNAs

The number of common miRNAs shared by a group of ceRNAs and mRNAs.

pvalue.cutoff

The p-value cutoff of significant sharing of common miRNAs by a group of ceRNAs and mRNAs.

CC.cutoff

The cutoff of cannonical correlation for 'CC' method.

SCC.cutoff

The cutoff of sensitivity cannonical correlation for 'SCC' method.

Value

List object: Cannonical correlation or sensitivity cannonical correlation, and genes of miRNA sponge modules.

Author(s)

Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)

References

Witten DM, Tibshirani R, Hastie T. A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics. 2009, 10(3):515-34.

Examples

data(BRCASampleData)
modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)], 
    mRExp[, seq_len(10)])
# Identify miRNA sponge modules using cannonical correlation (CC)
miRSM_igraph_CC <- miRSM(miRExp, ceRExp, mRExp, miRTarget,
                        modulegenes_igraph, nperms = 5,
                        method = 'CC')


[Package miRSM version 1.0.0 Index]