CELLector.CFEs.CNAid_decode: Decoding table for copy number alteration cancer functional...

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

Decoding table for copy number alteration cancer functional events

Description

A table with identifiers of cancer functional events (CFEs) involving chromosomal regions of recurrent copy number alterations (RACSs, as defined by [1], i.e. identified throgh ADMIRE [2]) and their annotation.

Usage

data("CELLector.CFEs.CNAid_decode")

Format

A data frame with 731 observations (one for each CNA CFE) on the following 15 variables.

Identifier

The RACS identifer, as defined in [1]

CancerType

A TCGA label indicating the cancer type where the RACS has been identified (via ADMIRE [2])

Recurrent

A string specifying whether the RACS under consideration is frequently amplified (value = Amplification) or deleted ) (value = deleted)

chr

Chromosome number of the RACS

start

Starting position of the RACS

stop

Ending position of the RACS

nGenes

Number of protein coding genes included in the RACS

locus

Genomic locus of the RACS

ContainedGenes

A string with comma separated symbols of the genes included in the RACS

CNA_Identifier

A string containing the identifer of the RACS as it appears in the Binary Event Matrix (BEM) of the cancer type specified in the CancerType field included in the

CELLector.CellLine.BEMs and the CELLector.PrimTum.BEMs data objects

Details

This data frame contains a comprehensive annotation of the CFEs involving RACSs appearing in the BEMs of cell lines and primary tumours, contained in the CELLector.CellLine.BEMs and the CELLector.PrimTum.BEMs data objects. 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.

This table is used by the CELLector.cna_look_up function to decode the identifier of CFE involving a RACS.

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] van Dyk, E., Reinders, M. J. T. & Wessels, L. F. A. A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control. Nucleic Acids Res. 41, e100 (2013).

See Also

CELLector.CellLine.BEMs, CELLector.PrimTum.BEMs, CELLector.cna_look_up

Examples

data(CELLector.CFEs.CNAid_decode)
head(CELLector.CFEs.CNAid_decode)

data(CELLector.CellLine.BEMs)
colnames(CELLector.CellLine.BEMs$COREAD)[8]

CELLector.cna_look_up(cna_ID = colnames(CELLector.CellLine.BEMs$COREAD)[8],
                      TCGALabel = 'COREAD',
                      cnaId_decode = CELLector.CFEs.CNAid_decode)

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