Analysis of co-knockdown data

This is the vignette to the R package coRNAi. coRNAi consists of functions for analysing combinatorial RNAi knockdown screens. The package builds on the R package cellHTS2 and takes a cellHTS object as input. In the section Creating cellHTS object for coRNAi, we will discuss the extra annotations needed for the downstream analysis of combinatorial knockdown data and we will provide an example of a valid annotation file for cellHTS2. In the section Analysis of co-RNAi screens we will illustrate the workflow by going through the analysis of two different datasets step by step. The section Moderated t-test provides justifications for the usage of a moderated t-test, in the section Choice of fitness phenotype we will briefly describe two possible fitness measurements. In the last section Analysis of large datasets we will show how it is possible to speed up the analysis when working with large and interaction sparse datasets.