CoRe.randomisedepMat: Column-wise matrix randomisation

In DepMap-Analytics/CoRe: CoRe R package

Column-wise matrix randomisation

Description

This function takes in input a matrix and shuffles its entries column-wise. Then matrix resulting from this shuffling will have the same column marginal totals of the inputted one.

Usage

CoRe.randomisedepMat(depMat)

Arguments

depMat

A numeric matrix

Value

The matrix given in input with entries shuffled column wisely.

Author(s)

C. Pacini, E. Karakoc, A. Vinceti & F. Iorio

References

[1] Behan FM, Iorio F, Picco G, Gonçalves E, Beaver CM, Migliardi G, et al. Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. Nature. 2019;568:511–6.

[2] Dwane L, Behan FM, Gonçalves E, Lightfoot H, Yang W, van der Meer D, Shepherd R, Pignatelli M, Iorio F, Garnett MJ. Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets. Nucleic Acids Res. 2021 Jan 8;49(D1):D1365-D1372.

Examples

## Downloading binary dependency matrix
## for > 300 cancer cell lines from Project Score [1,2]
BinDepMat<-CoRe.download_BinaryDepMatrix()

## Extracting dependency submatrix for
## Non-Small Cell Lung Carcinoma cell lines only
LungDepMat<-CoRe.extract_tissueType_SubMatrix(BinDepMat)

## Randomising the colums of the submatrix
rnd_exampleDepMat<-CoRe.randomisedepMat(LungDepMat)

DepMap-Analytics/CoRe documentation built on July 6, 2022, 8:01 a.m.