RTNmotifs-package: RTNduals: An R/Bioconductor package for analysis of...

Description Details Index Author(s) References

Description

RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer "dual regulons", a new concept that tests whether regulon pairs agree on the predicted downstream effects.

Details

Package: RTNduals
Type: Package
Depends: R (>= 3.4.0), methods, RTN
Imports: grDevices, stats, utils
Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
License: Artistic-2.0
biocViews: NetworkInference, NetworkEnrichment, GeneRegulation, GeneExpression, GraphAndNetwork

Index

MBR-class: an S4 class for co-regulation analysis and inference of 'dual regulons'.
mbrPreprocess: a preprocessing function for objects of class MBR.
mbrPermutation: inference of transcriptional networks.
mbrBootstrap: inference of consensus transcriptional networks.
mbrDpiFilter: a filter based on the Data Processing Inequality (DPI) algorithm.
mbrAssociation: motifs analysis and inference of "dual regulons".
mbrDuals: a summary for results from the MBR methods.
tni2mbrPreprocess: a preprocessing function for objects of class MBR.

Further information is available in the vignettes by typing vignette("RTNduals"). Documented topics are also available in HTML by typing help.start() and selecting the RTNduals package from the menu.

Author(s)

Vinicius S. Chagas, Clarice S. Groeneveld, Kerstin B Meyer, Gordon Robertson, Mauro A. A. Castro

References

Fletcher M.N.C. et al., Master regulators of FGFR2 signalling and breast cancer risk. Nature Communications, 4:2464, 2013.

Castro M.A.A. et al., Regulators of genetic risk of breast cancer identified by integrative network analysis. Nature Genetics, 48:12-21, 2016.


chagasVinicius/RTNmotifs documentation built on May 12, 2017, 2:15 a.m.