The package contains functions to organize the data from (single- and multi-parametric) genetic interaction screens. Methods to estimate main effects (single perturbation effects) and pairwise interactions. p-values are computed. Furthermore a comprehensive html-report is generated.
Details
See vignette("RNAinteract") for details.
Package content
Class RNAinteract (Documentation: RNAinteract-class)
Data input and creating of an object of class RNAinteract.
createCellHTSFromFiles
createRNAinteract, createRNAinteractFromFiles
Data access
getData Primary data access function for multiple types of screen data.
plotDoublePerturbation, plotHeatmap standard plot functions
doublePerturbationGrob, grid.doublePerturbation, grid.sgiHeatmap specialized grid plotting functions for experts
HTML report
startReport, endReport starting and finalizing a report
reportAnnotation, reportStatistics global reports
reportDoublePerturbation, reportGeneLists, reportHeatmap, reportMainEffects, reportNetworks, reportScreenData reports specific for each screen and each channel
Author(s)
Bernd Fischer
Maintainer: Bernd Fischer <bernd.fischer@embl.de>
References
T. Horn, T. Sandmann, B. Fischer, W. Huber, M. Boutros. Mapping of Signalling Networks through Synthetic
Genetic Interaction Analysis by RNAi. Nature Methods, 2011.