CoRe: CoRe R package

CoRe.extract_tissueType_SubMatrix

R Documentation

Subset Dependency Matrix based on tissue/cancer type of interest

Description

Extracting Dependency SubMatrix for a given tissue or cancer type.

Usage

CoRe.extract_tissueType_SubMatrix(fullDepMat,
                                         tissue_type="Non-Small Cell Lung Carcinoma")

Arguments

`fullDepMat`	Dependency Matrix containing all cell models. For example, downloadable from Project Score [1,2] using the function `CoRe.download_BinaryDepMatrix` or `CoRe.download_DepMatrix`.
`tissue_type`	Character, name of tissue/cancer type of interest. If the dependency matrix is from Project Score [1,2] this needs to be compatible with the nomeclature used in the Cell Model Passports [3]. Cell line annotations can be downloaded from the Cell Model Passports using the function `CoRe.download_AnnotationModel`.

Details

Extracting Dependency SubMatrix for a given tissue or cancer type, among those included in the latest model annotation file on the cell model passports [1][2].

Value

Dependency SubMatrix

cs_depmat

Dependency Submatrix containing data only for the cell lines from the tissue/cancer-type of interest.

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.

[3] Van der Meer D, Barthorpe S, Yang W, et al. Cell Model Passports—a hub for clinical, genetic and functional datasets of preclinical cancer models. Nucleic Acids Research 2019; 47(D1):D923–D929. doi:10.1093/nar/gky872.

Examples

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

## Subset Binary Dependency Matrix based on "Non-Small Cell Lung Carcinoma" cancer type
LungDepMat<-CoRe.extract_tissueType_SubMatrix(BinDepMat,tissue_type="Non-Small Cell Lung Carcinoma")

head(LungDepMat)

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