miRSM {miRSM} | R Documentation |
Identify miRNA sponge modules using cannonical correlation (CC) and sensitivity cannonical correlation (SCC) methods
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)
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. |
List object: Cannonical correlation or sensitivity cannonical correlation, and genes of miRNA sponge modules.
Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)
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.
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')