ccr.get.CCLEgisticSets: CCLE gistic score gene sets

In francescojm/CRISPRcleanR: Unsupervised correction of gene independent cell responses to CRISPR-cas9 targeting

CCLE gistic score gene sets

Description

This function splits all the genes into 5 classes (-2, -1, 0, +1 and +2) based on the CNA Gistic [1] score observed in a given cell line.

Usage

ccr.get.CCLEgisticSets(cellLine,CCLE.gisticCNA=NULL,GDSC.CL_annotation=NULL)

Arguments

cellLine	A string specifying the name of a cell line (or a COSMIC identifier [2]);
CCLE.gisticCNA	Genome-wide Gistic [1] scores quantifying copy number status across cell lines with the same format of CCLE.gisticCNA. If NULL then this function uses the CCLE.gisticCNA builtin data frame, containing data for 13 cell lines of the 15 used in [3] to assess the performances of CRISPRcleanR.
GDSC.CL_annotation	Cell lines annotation dataframe with the same structure of the GDSC.CL_annotation. If NULL then the GDSC.CL_annotation is used.

Value

A named list of vectors with the following fields:

gm2	A vector of strings containing identifiers of sgRNAs targeting genes whit a Gistic score = -2 in the cell line under consideration;
gm1	A vector of strings containing identifiers of sgRNAs targeting genes whit a Gistic score = -1 in the cell line under consideration;
gz	A vector of strings containing identifiers of sgRNAs targeting genes whit a Gistic score = 0 in the cell line under consideration;
gp1	A vector of strings containing identifiers of sgRNAs targeting genes whit a Gistic score = +1 in the cell line under consideration;
gp2	A vector of strings containing identifiers of sgRNAs targeting genes whit a Gistic score = +2 in the cell line under consideration;

Author(s)

Francesco Iorio ([e-mail])

References

[1] Mermel CH, Schumacher SE, Hill B, et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 2011;12(4):R41. doi: 10.1186/gb-2011-12-4-r41.

[2] Forbes SA, Beare D, Boutselakis H, et al. COSMIC: somatic cancer genetics at high-resolution Nucleic Acids Research, Volume 45, Issue D1, 4 January 2017, Pages D777-D783,

[3] Iorio, F., Behan, F. M., Goncalves, E., Beaver, C., Ansari, R., Pooley, R., et al. (n.d.). Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting.
http://doi.org/10.1101/228189

See Also

ccr.get.gdsc1000.AMPgenes

Examples

GS<-ccr.get.CCLEgisticSets('HT-29')

head(GS$gm2)
head(GS$gm1)
head(GS$gz)
head(GS$gp1)
head(GS$gp2)

francescojm/CRISPRcleanR documentation built on April 30, 2023, 5:41 a.m.