GDSC.geneLevCNA: Genome-wide copy number data for 15 human cancer cell lines.

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

Genome-wide copy number data for 15 human cancer cell lines.

Description

Genome-wide copy number data derived from PICNIC analysis of Affymetrix SNP6 segmentation data (EGAS00001000978, part of the Genomics of Drug Sensitivity in 1,000 Cancer Cell Lines (GDSC1000) panel [1]) for 15 cell lines used in [2] to assess CRISPRcleaneR results.

Usage

data(GDSC.geneLevCNA)

Format

A data frame with HGNC gene symbols on the row cancer cell lines' cosmic identifiers on the columns. The entry in position i,j indicates the copy number status of gene i in cell line j.

Details

Each entry of the data frame is a string made of four comma seperated peices of data (n1,n2,n3,n4), hyphen (-) is used when the corresponding data is unknown.

The four values indicate:

• n1: Maximum copy number of any genomic segment containing coding sequence of the gene (-1 indicates a value could not be assigned).

• n2: Minimum copy number of any genomic segment containing coding sequence of the gene (-1 indicates a value could not be assigned).

• n3: Zygosity - (H) if all segments containing gene sequence are heterozygous, (L) if any segment containing coding sequence has LOH, (0) if the complete coding sequence of the gene falls within a homozygous deletion.

• n4: Disruption (D) if the gene spans more than 1 genomic segment (-) if no disruption occures.

Source

This data frame has been derived from the xls table available at ftp://ftp.sanger.ac.uk/pub/project/cancerrxgene/releases/release-6.0/Gene_level_CN.xlsx.

References

[1] 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

[2] 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

Examples

data(GDSC.geneLevCNA)
GDSC.geneLevCNA[1:10,1:10]

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