CoRe.AssembleFPs: Assembling expression-based false positives

In DepMap-Analytics/CoRe: CoRe R package

Assembling expression-based false positives

Description

Assembling a set of lowly expressed genes cancer cell lines from the CCLE [1].

Usage

CoRe.AssembleFPs(URL='https://ndownloader.figshare.com/files/26261476')

Arguments

URL	URL of the CCLE gene expression dataset.

Details

This function download CCLE gene expression data from DepMap portal [1] then it estimates a set of overall lowly expressed genes as detailed in [2].

Value

LowlyExpr

A vector of strings with symbols of genes that are lowly expressed across ~1,300 cell lines to be used as false positive by the benchmarking function.

Author(s)

A. Vinceti & F. Iorio

References

[1] Barretina, J., Caponigro, G., Stransky, N. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012).

[2] Pacini, Dempster et al, Integrated cross-study datasets of genetic dependencies in cancer. https://doi.org/10.1101/2020.05.22.110247 .

See Also

CoRe.CF_Benchmark

Examples

FPs<-CoRe.AssembleFPs()
head(FPs)

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