CELLector.PrimTumVarCatalog: Built-in Primary Tumour variants' catalogue

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

Built-in Primary Tumour variants' catalogue

Description

List of somatic variants found in primary tumours, from Iorio et al, Cell 2016 [1]

Usage

data("CELLector.PrimTumVarCatalog")

Format

A data frame with 727228 observations (one for each somatic variants) on the following 12 variables.

SAMPLE

a character vector specifying the identifier of the sample in which the variant has been found

Cancer.Type

a character vector specifying the TCGA [2] classification of the tissue of origin of the tumour in which the variant has been found

Gene

a character vector specifying the HUGO [3] symbol of the gene hosting the variant under consideration

Transcript

a character vector specifying the identifier of the transcript affected by the variant under consideration

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 Primary tumours' Binary Event Matrices (BEMs)

Recurrence.Filter

a character vector: if 'Yes' then the variant under consideration is observed in COSMIC [4] (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)

References

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

[2] 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

[3] 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

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

Examples

data(CELLector.PrimTumVarCatalog)
head(CELLector.PrimTumVarCatalog)

najha/CELLector documentation built on Feb. 8, 2023, 5:35 a.m.