CELLector.CellLinesVarCatalog: Built-in Cell Line variants' catalogue

In najha/CELLector: Genomics guided selection of cancer cell lines

Built-in Cell Line variants' catalogue

Description

List of somatic variants found in cell-lines, from Iorio et al, Cell 2016 [1]

Usage

data("CELLector.CellLinesVarCatalog")

Format

A data frame with 486243 observations (one for each somatic variants) on the following 13 variables.

SAMPLE

a character vector specifying the name of the cell line in which the variant has been found

COSMIC_ID

a numeric vector specifying COSMIC [2] identifier of the cell line in which the variant has been found

Cancer.Type

a character vector specifying the TCGA [3] classification of the tissue of origin of the cell line in which the variant has been found

Gene

a character vector specifying the HUGO [4] symbol of the gene hosting the variant under consideration (from Ensemble v56)

Transcript

a character vector specifying the identifier of the transcript affected by the variant under consideration (from Ensemble v56)

cDNA

a character vector specifying variant position and nucleotide change relating to the cDNA

AA

a character vector specifying aminoacid positon and alteration related to the variant under consideration

Classification

a character vector specifying a summary of the variant type (e.g. missense, frameshift, nonsense, etc)

Gene_list

a character vector: when non empty then the variant is within a high-confidence cancer driver gene (according to [1]), thus resulting in a cancer functional event (CFE) summarised in the Cell line Binary Event Matrices (BEMs)

Recurrence.Filter

a character vector: if 'Yes' then the variant under consideration is observed in COSMIC [2] (v68) at a minimal threshold frequency (specified in [1])

Subs

a numeric vector: Missense/substitution variants occurring in codons mutated in the systematic screen data in COSMIC [2] (v68) (select >=3

Truncating

a numeric vector: Truncating variant count from the systematic screen data in COSMIC [2] (v68) (select >10)

inframe

a numeric vector: Inframe indel alterations occurring in codons mutated in the systematic screen data in COSMIC [2] (v68) (select >=3)

Author(s)

Francesco Iorio ([e-mail])

References

[1] Iorio, F. et al. A Landscape of Pharmacogenomic Interactions in Cancer. Cell 166, 740–754 (2016).

[2] Forbes, S. A. et al. COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805–11 (2015).

[3] Hutter C and Zenklusen JC. The Cancer Genome Atlas: Creating Lasting Value beyond Its Data. Cell. 2018;173(2):283–285. doi:10.1016/j.cell.2018.03.042

[4] Braschi, B. et al. Genenames.org: the HGNC and VGNC resources in 2019. Nucleic Acids Res. Epub 2018 Oct 10. PMID: 30304474 DOI: 10.1093/nar/gky930

See Also

CELLector.CellLine.BEMs, CELLector.CellLine.BEMs_v2, CELLector.CFEs

Examples

data(CELLector.CellLinesVarCatalog)
head(CELLector.CellLinesVarCatalog)

najha/CELLector documentation built on Sept. 4, 2024, 10:17 p.m.