copyNumber: copyNumber_22Q2

In UCLouvain-CBIO/depmap: Cancer Dependency Map Data Package

copyNumber_22Q2

Description

The 'copyNumber' dataset contains the 22Q2 inferred copy number data for genes and cancer cell lines. This dataset includes data from 25368 genes, 1754 cell lines, 35 primary diseases and 38 lineages. The columns of 'copyNumber' are: 'depmap_id', a foreign key corresponding to the cancer cell lineage, 'cell_line' containing the common CCLE name of the cancer cell lines, 'gene' containing both the HUGO gene name of the knockdown gene along with entrez ID#, 'gene_name' containing only the HUGO gene name, 'entrez_id' containing only the entrez ID#, and 'log_copy_number' containing the numerical dependency score values for each pair of genes and cell lines. This dataset can be loaded into the R environment with the 'depmap_copyNumber' function.

Usage

copyNumber

Format

A data frame with 44799888 rows (cell lines) and 6 variables.

depmap_id

Cancer cell line foreign key (i.e. "ACH-00001")

gene

HUGO symbol (e.g. "SAP25") and Entrez ID# (e.g. 100316904)

gene_name

HUGO symbol (e.g. "SAP25")

entrez_id

Entrez ID# (e.g. 100316904)

log_copy_number

numerical log fold change in copy number for a given gene and cell line

cell_line

CCLE name of cancer cell line (i.e. "184A1_BREAST")

Details

This data represents the 'CCLE_gene_cn.csv' file taken from the 22Q2 [Broad Institute](https://depmap.org/portal/download/) cancer depenedency study. The derived dataset found in the 'depmap' package features the addition of a foreign key 'depmap_id' found in the first column of this dataset, which was added from the 'metadata' dataset. This dataset has been converted to a long format tibble. Variables names from the original dataset were converted to lower case, put in snake case, and abbreviated where feasible.

Change log

- 19Q1: Initial dataset consisted of a data frame with 37907473 rows (cell lines) and 6 variables representing 23299 genes, 1604 cell lines, 38 primary diseases and 33 lineages.

- 19Q2: adds 23 cell lines and 1 lineage

- 19Q3: adds 3263 genes, 30 cell lines and removes 2 primary diseases. Now a dataframe with 45670234 rows and 6 variables

- 19Q4: adds 77 genes, 25 cell lines, 0 primary diseases and 2 lineages

- 20Q1: adds 31 cell lines

- 20Q2: adds 32 cell lines

- 20Q3: no change

- 20Q4: removes 77 genes, adds 8 cell lines and 1 lineage

- 21Q1: removes 13 cell lines

- 21Q2: adds 2 cell lines

- 21Q3: removes 1 cell line and 1 lineage

- 21Q4: removes 194 genes and adds 9 cell lines

- 22Q1: removes 2000 genes, adds 4 cell lines and 1 lineage

- 22Q2: adds 12 cell lines and removes 2 primary diseases and 8 lineages

Source

DepMap, Broad Institute: https://depmap.org/portal/download/

References

Tsherniak, A., Vazquez, F., Montgomery, P. G., Weir, B. A., Kryukov, G., Cowley, G. S., ... & Meyers, R. M. (2017). Defining a cancer dependency map. Cell, 170(3), 564-576.

DepMap, Broad (2019): DepMap Achilles 19Q1 Public. https://figshare.com/articles/DepMap_Achilles_19Q1_Public/7655150

Robin M. Meyers, Jordan G. Bryan, James M. McFarland, Barbara A. Weir, ... David E. Root, William C. Hahn, Aviad Tsherniak. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nature Genetics 2017 October 49:1779–1784.

Mahmoud Ghandi, Franklin W. Huang, Judit Jané-Valbuena, Gregory V. Kryukov, ... Todd R. Golub, Levi A. Garraway & William R. Sellers. 2019. Next- generation characterization of the Cancer Cell Line Encyclopedia. Nature 569, 503–508 (2019).

Examples

## Not run: 
depmap_copyNumber()

## End(Not run)

UCLouvain-CBIO/depmap documentation built on March 24, 2024, 2 p.m.