CELLector.CFEsV2: Cancer Functional Events (version 2)

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

Cancer Functional Events (version 2)

Description

Identifiers of cancer functional events (CFEs, i.e. somatic mutations in high confidence cancer driver genes, chromosomal regions of recurrent copy number amplification/deletion, and informative hypermethylated gene promoters) from [1], which are also present in the binary event matrices (version 2) of the cell lines and the primary tumours considered in this version of CELLector.

Usage

data("CELLector.CFEsV2")

Format

A vector of strings with one entry per identifier.

Details

Gene symbols indicate somatic mutations in high confidence cancer driver genes, entries with cna prefix indicate chromosomal segments that are recurrently copy number altered in cancer (RACSs), entries with hms prefix indicate hypermehylated gene promoters, all defined in [1].

A decoding table for the HMS is available in the CELLector.CFEs.HMSid_decode object, with the mapping realised by the values in the hms_id column.

Please note that the same RACS identifier across multiple cancer types might indicate different chromosomal regions, therefore in order to be decode it should be considered jointly with the TCGA label of the data frame it has been extracted from.

Author(s)

Francesco Iorio ([e-mail])

References

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

See Also

CELLector.PrimTum.BEMs_v2, CELLector.CellLine.BEMs_v2, CELLector.CFEs, CELLector.CFEs.CNAid_decode, CELLector.CFEs.HMSid_decode

Examples

data(CELLector.CFEsV2)
head(CELLector.CFEsV2)

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