CoRe.download_BinaryDepMatrix: Download Binary Dependency Matrix

In DepMap-Analytics/CoRe: CoRe R package

Download Binary Dependency Matrix

Description

Downloading Binary Dependency Matrix introduced in [1] from the Project Score portal [2].

Usage

CoRe.download_BinaryDepMatrix(
URL='https://cog.sanger.ac.uk/cmp/download/binaryDepScores.tsv.zip')

Arguments

URL	URL pointing to the online location of a zipped folder containing a binary dependency matrix. By default this will point to an entry on the data download page of the Project Score portal with data from [1].

Details

If the URL points to a valid online location this function downloads a Binary Dependency Matrix.

Value

A binary Dependency Matrix (from [1]) where rows are genes and columns are cell lines. A 1 in position [i,j] indicates that the inactivation of the i-th gene exerts a significant loss of fitness in the j-th sample, 0 otherwise.

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, et al. 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 [1,2]
BinDepMat<-CoRe.download_BinaryDepMatrix()

head(BinDepMat)

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