Roleswitch: Infer miRNA-mRNA interactions using paired expression data from a single sample

Infer Probabilities of MiRNA-mRNA Interaction Signature (ProMISe) using paired expression data from a single sample. Roleswitch operates in two phases by inferring the probability of mRNA (miRNA) being the targets ("targets") of miRNA (mRNA), taking into account the expression of all of the mRNAs (miRNAs) due to their potential competition for the same miRNA (mRNA). Due to dynamic miRNA repression in the cell, Roleswitch assumes that the total transcribed mRNA levels are higher than the observed (equilibrium) mRNA levels and iteratively updates the total transcription of each mRNA targets based on the above inference. NB: in the paper, we used ProMISe as both the model name and inferred score name.

Author
Yue Li
Date of publication
None
Maintainer
Yue Li <yueli@cs.toronto.edu>
License
GPL-2
Version
1.12.0
URLs

View on Bioconductor

Man pages

diagnosticPlot
Create diagnostic plot for understanding the Roleswitch model...
getSeedMatrix
Get seed-match matrix between defined mRNA and miRNA in an...
roleswitch
Infer miRNA-mRNA interactions using paired expression data...
Roleswitch-package
Infer miRNA-mRNA interactions using paired expression data...
tcga_gbm_testdata
Test data of miRNA and mRNA expression vector.

Files in this package

Roleswitch/DESCRIPTION
Roleswitch/NAMESPACE
Roleswitch/R
Roleswitch/R/diagnosticPlot.R
Roleswitch/R/getSeedMatrix.R
Roleswitch/R/roleswitch.R
Roleswitch/build
Roleswitch/build/vignette.rds
Roleswitch/data
Roleswitch/data/datalist
Roleswitch/data/tcga_gbm_testdata.RData
Roleswitch/inst
Roleswitch/inst/CITATION
Roleswitch/inst/NEWS
Roleswitch/inst/doc
Roleswitch/inst/doc/Roleswitch.R
Roleswitch/inst/doc/Roleswitch.Rnw
Roleswitch/inst/doc/Roleswitch.pdf
Roleswitch/man
Roleswitch/man/Roleswitch-package.Rd
Roleswitch/man/diagnosticPlot.Rd
Roleswitch/man/getSeedMatrix.Rd
Roleswitch/man/roleswitch.Rd
Roleswitch/man/tcga_gbm_testdata.Rd
Roleswitch/vignettes
Roleswitch/vignettes/Roleswitch.Rnw
Roleswitch/vignettes/Roleswitch.bib