Statistical Analysis of High-Throughput Genetic Perturbation Screens

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Documentation for package ‘perturbatr’ version 1.12.0

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perturbatr-package perturbatr
bootstrap Create a bootstrap sample from a data-set
dataSet Getter for a data set
dataSet-method Getter for a data set
diffuse Network diffusion
diffuse-method Network diffusion
filter Filter the rows of a perturbation data set
geneEffects Getter for the complete list of genes and their effect sizes
geneEffects-method Getter for the complete list of genes and their effect sizes
graph Getter for graph used for network diffusion
graph-method Getter for graph used for network diffusion
hm Jointly analyse multiple genetic perturbation screens using a hierarchical model
hm-method Jointly analyse multiple genetic perturbation screens using a hierarchical model
HMAnalysedPerturbationData-class Data wrapper for analysed perturbation data using a hierarchical model
inference Getter for inference used for analysis of perturbation data
inference-method Getter for inference used for analysis of perturbation data
isBootstrapped Getter for boolean if boostrapping was used
isBootstrapped-method Getter for boolean if boostrapping was used
modelFit Getter for model fit
modelFit-method Getter for model fit
nestedGeneEffects Getter for the completed list of nested gene effects
nestedGeneEffects-method Getter for the completed list of nested gene effects
NetworkAnalysedPerturbationData-class Data wrapper for analysed perturbation data using network diffusion
params Getter for parameters used for analysis of perturbation data
params-method Getter for parameters used for analysis of perturbation data
PerturbationData-class Data wrapper for a data set of a perturbation screen.
plot.NetworkAnalysedPerturbationData Plot a 'NetworkAnalysedPerturbationData' object
plot.PerturbationData Plot perturbation data
rbind.PerturbationData Bind multiple perturbation data sets together by row
rnaiscreen A sample pan-pathogenic perturbation dataset
setModelData Create model data for an hierarchical model
setModelData-method Create model data for an hierarchical model