RNAinteract-package {RNAinteract} | R Documentation |
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.
See vignette("RNAinteract") for details.
Class RNAinteract
(Documentation: RNAinteract-class
)
Data input and creating of an object of class RNAinteract
.
Data access
getData
Primary data access function for multiple types of screen data.
getMain
, getMainNeg
access to main effects.
getReplicateData
, getIndDesignData
Comparing replicate data.
Subsetting, summarizing, and binding screens
Main effects and pairwise interactions
Plotting
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
Bernd Fischer
Maintainer: Bernd Fischer <bernd.fischer@embl.de>
T. Horn, T. Sandmann, B. Fischer, W. Huber, M. Boutros. Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi. Nature Methods, 2011.