rnai: rnai_19Q3

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

rnai_19Q3

Description

The 'rnai' dataset contains the 19Q3 cancer dependency of select cancer cell lines for genes found by RNAi gene knockdown. This dataset includes data from 17309 genes, 712 cancer cell lines, 31 primary diseases and 31 lineages. The columns of 'rnai' 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' which only contains HUGO gene name, 'entrez_id' which contains only the entrez ID# and 'dependency' which contains 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_rnai' function.

Usage

rnai

Format

A data frame with 12324008 rows (cell lines) and 6 variables:

depmap_id

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

cell_line

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

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)

dependency

numerical depenency score of a gene for a cell line

Details

This data represents the 'D2_combined_genetic_dependency_scores' file taken from the 19Q3 [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 12324008 rows (cell lines) and 6 variables representing 17309 genes, 711 cancer cell lines, 30 primary diseases and 31 lineages.

- 19Q2: adds 1 cell line

- 19Q3: adds 1 primary disease

- 19Q4: no change, no further releases are scheduled at this time. NOTE: as of this release, the crispr dataset replaces the rnai dataset for dependency measurements in all future releases.

- 20Q1: no change, this dataset is superceded by the CRISPR dependency screens and no further releases are scheduled.

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.

James M. McFarland, Zandra V. Ho, Guillaume Kugener, Joshua M. Dempster, Phillip G. Montgomery, Jordan G. Bryan, John M. Krill-Burger, Thomas M. Green, Francisca Vazquez, Jesse S. Boehm, Todd R. Golub, William C. Hahn, David E. Root, Aviad Tsherniak. (2018). Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nature Communications 9, 1.

Examples

## Not run: 
depmap_rnai()

## End(Not run)

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