RNAinteract (version 1.20.0)

RNAinteract-package: Analysis of Pairwise Interaction Screens.

Description

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.

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.
• getMain, getMainNeg access to main effects.
• getReplicateData, getIndDesignData Comparing replicate data.
• getChannelNames, getScreenNames, getScale

Subsetting, summarizing, and binding screens

• sgisubset, sgisubsetQueryDesign
• bindscreens
• summarizeScreens

Main effects and pairwise interactions

• estimateMainEffect
• normalizeMainEffectQuery, normalizeMainEffectTemplate, normalizePlateEffect
• computePI, computePValues
• embedPCA

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

Details

See vignette("RNAinteract") for details.

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.