RNAinteract: Estimate Pairwise Interactions from multidimensional features
Version 1.24.0

RNAinteract estimates genetic interactions from multi-dimensional read-outs like features extracted from images. The screen is assumed to be performed in multi-well plates or similar designs. Starting from a list of features (e.g. cell number, area, fluorescence intensity) per well, genetic interactions are estimated. The packages provides functions for reporting interacting gene pairs, plotting heatmaps and double RNAi plots. An HTML report can be written for quality control and analysis.

Browse man pages Browse package API and functions Browse package files

AuthorBernd Fischer <b.fischer@dkfz.de>
Bioconductor views CellBasedAssays Preprocessing QualityControl Visualization
Date of publicationNone
MaintainerBernd Fischer <b.fischer@dkfz.de>
LicenseArtistic-2.0
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RNAinteract")

Man pages

bindsamples: bind RNAinteract objects along screens
computePI: compute pairwise interaction
computePValues: compute p-values
createCellHTSFromFiles: create cellHTS2 object from text files
createRNAinteract: create a RNAinteract object
createRNAinteractFromFiles: create an RNAinteract object from text files
embedPCA: Computes a PCA for a pairwise interaction matrix.
estimateMainEffect: estimate main effect
getData: Primary access function for all screen data.
getMain: get main effects
getReplicateData: Extract replicates measurements from the screen.
getSampleNames: get names of screens and channels
getScale: get scale information for a channel.
grid.doublePerturbation: Double Perturbation Plot Grob
grid.sgiHeatmap: A heatmap grob
normalizeMainEffectQuery: normalize query main effect
normalizeMainEffectTemplate: normalize template main effect
normalizePlateEffect: Normalization of plate effects
plotDoublePerturbation: Double Perturbation Plot
plotHeatmap: plots a heatmap for an interaction screen.
reportAnnotation: Specialized report functions
RNAinteract-class: Class "RNAinteract"
RNAinteract-package: Analysis of Pairwise Interaction Screens.
sgi: Dataset of class 'RNAinteract'
sgisubset: subset of an RNAinteract object.
sgisubsetQueryDesign: Subsetting query genes in a RNAinteract object.
startReport: start and end a RNAinteract report
summarizeSamples: summarize screens
swaptree: Swaps a branch of a hclust object.

Functions

RNAinteract Man page
RNAinteract-class Man page
RNAinteract-package Man page
bindscreens Man page Source code
computePI Man page Source code
computePValues Man page Source code
createCellHTSFromFiles Man page Source code
createRNAinteract Man page Source code
createRNAinteractFromFiles Man page Source code
doublePerturbationGrob Man page Source code
embedPCA Man page Source code
endReport Man page Source code
estimateMainEffect Man page Source code
getChannelNames Man page Source code
getData Man page Source code
getDoublePerturbationLabels Source code
getIndDesignData Man page Source code
getInvTransformation Source code
getMain Man page Source code
getMainNeg Man page Source code
getReplicateData Man page Source code
getScale Man page Source code
getScreenNames Man page Source code
getTransformation Source code
grid.doublePerturbation Man page Source code
grid.sgiColorkey Source code
grid.sgiDendrogram Source code
grid.sgiHeatmap Man page Source code
grid.sgiHeatmap.2 Source code
invtransform Source code
makeDoublePerturbationAxis Source code
makeDoublePerturbationLabels Source code
makeDoublePerturbationMain Source code
makeDoublePerturbationMainEffects Source code
makeDoublePerturbationNI Source code
makeDoublePerturbationPoints Source code
makeDoublePerturbationVP Source code
makeDoublePerturbationWTlines Source code
normalizeMainEffectQuery Man page Source code
normalizeMainEffectTemplate Man page Source code
normalizePlateEffect Man page Source code
ordertree Source code
plotDoublePerturbation Man page Source code
plotHeatmap Man page Source code
plotIndDesignScatter Source code
plotMainEffects Source code
plotReplicateScatter Source code
plotScatterErrorbars Source code
plotScreenData Source code
postDrawDetails.doublePerturbation Man page Source code
reportAnnotation Man page Source code
reportDoublePerturbation Man page Source code
reportGeneLists Man page Source code
reportHeatmap Man page Source code
reportMainEffects Man page Source code
reportNetworks Man page Source code
reportScreenData Man page Source code
reportStatistics Man page Source code
sgi Man page
sgisubset Man page Source code
sgisubsetQueryDesign Man page Source code
shiftboxes Source code
show,RNAinteract-method Man page
startReport Man page Source code
summarizeScreens Man page Source code
swaptree Man page Source code
transform Source code
zPrime Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClass.R
R/computePvalue.R
R/createCellHTS.R
R/createRNAinteract.R
R/dataAccess.R
R/grid.doublePerturbation.R
R/grid.sgiHeatmap.R
R/mainEffects.R
R/normalization.R
R/plotDoublePerturbation.R
R/plotHeatmap.R
R/report.R
R/reportAnnotation.R
R/reportDoublePerturbation.R
R/reportGeneLists.R
R/reportHeatmap.R
R/reportMainEffects.R
R/reportNetworks.R
R/reportPCA.R
R/reportScreenSGI.R
R/reportStatistics.R
R/subsetting.R
R/transformation.R
build
build/vignette.rds
data
data/sgi.rda
inst
inst/CITATION
inst/RNAinteractExample
inst/RNAinteractExample/DataRNAinteractExample_1.txt
inst/RNAinteractExample/DataRNAinteractExample_2.txt
inst/RNAinteractExample/Platelist.txt
inst/RNAinteractExample/QueryDesign.txt
inst/RNAinteractExample/Reagents.txt
inst/RNAinteractExample/Targets.txt
inst/RNAinteractExample/TemplateDesign.txt
inst/RNAinteractExample/networks.txt
inst/doc
inst/doc/RNAinteract.R
inst/doc/RNAinteract.Rnw
inst/doc/RNAinteract.pdf
inst/makeExample
inst/makeExample/makeExample.Rnw
man
man/RNAinteract-class.Rd
man/RNAinteract-package.Rd
man/bindsamples.Rd
man/computePI.Rd
man/computePValues.Rd
man/createCellHTSFromFiles.Rd
man/createRNAinteract.Rd
man/createRNAinteractFromFiles.Rd
man/embedPCA.Rd
man/estimateMainEffect.Rd
man/getData.Rd
man/getMain.Rd
man/getReplicateData.Rd
man/getSampleNames.Rd
man/getScale.Rd
man/grid.doublePerturbation.Rd
man/grid.sgiHeatmap.Rd
man/normalizeMainEffectQuery.Rd
man/normalizeMainEffectTemplate.Rd
man/normalizePlateEffect.Rd
man/plotDoublePerturbation.Rd
man/plotHeatmap.Rd
man/reportAnnotation.Rd
man/sgi.Rd
man/sgisubset.Rd
man/sgisubsetQueryDesign.Rd
man/startReport.Rd
man/summarizeSamples.Rd
man/swaptree.Rd
vignettes
vignettes/RNAinteract.Rnw
RNAinteract documentation built on May 20, 2017, 10:41 p.m.