ccr.get.gdsc1000.AMPgenes: Copy number amplified genes in a given cell line from the...

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

Copy number amplified genes in a given cell line from the GDSC1000

Description

This function takes in input the name (or the COSMIC identifier [1]) of a cell line included in the GDSC1000 project [2] and it identifies the genes that are copy number amplified (according to a user defined minimal copy number value) in that cell line, using gene level copy number data from the Genomics of Drug Sensitivity in 1,000 Cancer Cell lines (GDSC1000) [2].

Usage

ccr.get.gdsc1000.AMPgenes(cellLine, minCN = 8, exact = FALSE,
                          GDSC.geneLevCNA=NULL,GDSC.CL_annotation=NULL)

Arguments

cellLine	A string specifying the name of a cell line (or a COSMIC identifier [1]);
minCN	Lower threshold for the minimum copy number of any genomic segment containing coding sequence of a gene in order for it to be considered as copy number amplified.
exact	If TRUE, then those genes for which any genomic segment containing coding sequence has a minimum copy number equal to minCN are considered as copy number amplified.
GDSC.geneLevCNA	Genome-wide copy number data with the same format of GDSC.geneLevCNA. This can be assembled from the xls sheet specified in the source section [a] (containing data for the GDSC1000 cell lines). If NULL, then this function uses the data in the built in GDSC.geneLevCNA data frame, containing data derived from [a] for 15 cell lines 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 data frame, containing one row for each copy number amplified gene with the following columns:

Gene	HGNC symbol of the gene;
minCN	Minimum copy number of any genomic segment containing coding sequence of the gene in the cell line under consideration.

Author(s)

Francesco Iorio ([e-mail])

Source

[a] ftp://ftp.sanger.ac.uk/pub/project/cancerrxgene/releases/release-6.0/Gene_level_CN.xlsx.

References

[1] 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,

[2] Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, et al. A landscape of pharmacogenomic interactions in cancer Cell 2016 Jul 28;166(3):740-54

[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.CCLEgisticSets

Examples

CNAgenes<-
    ccr.get.gdsc1000.AMPgenes('HT-29')
head(CNAgenes)

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