CoRe.scale_to_essentials: Scale matrix cell-wise using positive and negative reference...

In DepMap-Analytics/CoRe: CoRe R package

Scale matrix cell-wise using positive and negative reference gene sets

Description

This function takes as input a continuous dependency matrix and perform a cell-wise (i.e. column-wise) scaling by employing two reference sets of essential and nonessential genes.

Usage

CoRe.scale_to_essentials(ge_fit,
                         ess_genes,
                         noness_genes)

Arguments

ge_fit	Dependency matrix, rows are genes and columns are samples (screens, cell-cell lines).
ess_genes	Character vector, list of reference essential genes.
noness_genes	Character vector, list of reference nonessential genes.

Details

This function takes as input a continuous dependency matrix and perform a cell-wise (i.e. column-wise) scaling by setting, in every cell line, the median of reference essential genes to -1 and the median of reference non-essential genes to 0.

Value

scaled_ge_fit

Scaled dependency matrix.

Author(s)

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

References

[1] J. M. Dempster et al., Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets., Nat. Commun., vol. 10, no. 1, p. 5817, 2019, doi: 10.1038/s41467-019-13805-y.

[2] Clare Pacini et al., Integrated cross-study datasets of genetic dependencies in cancer., Nat. Commun., vol. 12, p. 1661, 2021, doi: 10.1038/s41467-021-21898-7.

See Also

CoRe.download_DepMatrix

Examples

data('curated_BAGEL_essential')
data('curated_BAGEL_nonEssential')

DepMat<-CoRe.download_DepMatrix()
scaled_DepMat<-CoRe.scale_to_essentials(DepMat,
                                        curated_BAGEL_essential,
                                        curated_BAGEL_nonEssential)

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