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.

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.

• 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

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.