rnaiscreen {perturbatr} | R Documentation

## A sample pan-pathogenic perturbation dataset

### Description

Example `PerturbationData` object of two integrated viral RNAi screens that consists of a HCV kinome screen and a SARS kinome screen (see references).

### Usage

    data(rnaiscreen)

### Format

A `PerturbationData` object containing a `tibble` with 18 columns, each describing a feature.

### Author(s)

Simon Dirmeier | Computational Biology Group, ETH ZURICH | simon.dirmeier@web.de

### References

de Wilde, Adriaan H., et al. (2015), A kinome-wide small interfering RNA screen identifies proviral and antiviral host factors in severe acute respiratory syndrome coronavirus replication, including double-stranded RNA-activated protein kinase and early secretory pathway proteins.
Journal of virology
Reiss, Simon, et al. (2011), Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment.
Cell Host & Microbe

Friedman J., Hastie T., Hoefling H. and Tibshirani R. (2007), Pathwise coordinate optimization.
The Annals of Applied Statistics

- Condition `character` names of the viruses

- Replicate `integer` replicate numer

- Plate `integer` plate index

- RowIdx `integer` row index of the well on the plate

- ColIdx `integer` column index of the well on the plate

- GeneSymbol `character` HugoSymbol of a gene

- Entrez `integer` entrez ID

- ReadoutType `character` readout type, such as 'GFP' or 'Luciferase'

- Control `integer` coding of controls. '-1' for negative control, '1' for positive control, '0' for regular sample

- Library `character` library type, such as 'Ambion'

- Perturbation `character` sirna identifier

- Screen `character` identifier, for example 'Kinome' or 'Genome'

- Cell `character` cell type, such as 'Huh7.5'

- ScreenType `character` screen type, such as 'E/R' for entry/replication

- Design `character` design of the library, e.g. 'pooled'

- Readout `numeric` readout value, e.g. GFP measurement or read count

- ReadoutClass `character` class of the readout, such as 'Readout' or 'Viability'

- NumCells `integer` number of measured cells per well

### Examples

     data(rnaiscreen)
     fit <- hm(rnaiscreen)
     pls <- plot(fit)
     pls[[1]]

[Package perturbatr version 1.10.0 Index]