mutationCalls: mutationCalls_22Q2

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

mutationCalls_22Q2

Description

The 'mutationCalls' dataset contains merged the 22Q2 mutation calls (for coding region, germline filtered) and includes data from 18784 genes, 1771 cell lines, 33 primary diseases and 30 lineages. This dataset can be considered the metadata data set for mutations and does not contain any dependency data. This dataset can be loaded into the R environment with the 'depmap_mutationCalls' function.

Usage

mutationCalls

Format

A data frame with 1235466 rows and 32 variables:

depmap_id

depmap_id

gene_name

Hugo Symbol denotes a unique and meaningful name for each gene (e.g. SAP25)

entrez_id

Gene ID for NCBI Entrez gene database, (e.g. 100316904)

ncbi_build

NCBI Build (i.e. reference genome)

chromosome

Chromosome

start_pos

Gene start position

end_pos

Gene end position

strand

Strand location of gene

var_class

Variant Classification

var_type

Variant Type

ref_allele

Reference Allele

alt_allele

Tumor Seq Allele1

dbSNP_RS

Single Nucleotide Polymorphism Database (dbSNP) reference cluster

dbSNP_val_status

dbSNP Val Status

genome_change

Genome Change

annotation_transcript

Annotation Transcript

cDNA_change

change in cDNA

codon_change

Codon_Change

protein_change

Protein_Change

is_deleterious

Status of gene knockout on cell lineage

is_tcga_hotspot

isTCGAhotspot

tcga_hsCnt

TCGAhsCnt

is_cosmic_hotspot

isCOSMIChotspot

cosmic_hsCnt

COSMIChsCnt

ExAC_AF

ExAC_AF

CGA_WES_AC

CGA_WES_AC

sanger_WES_AC

SangerWES_AC

RNAseq_AC

RNAseq_AC

HC_AC

HC_AC

RD_AC

RD_AC

WGS_AC

WGS_AC

var_annotation

Variant_annotation

Details

This data represents the 'CCLE_mutations.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 for package consisted of dataframe with 1243145 rows and 35 variables representing 18755 genes, 1601 cell lines, 37 primary diseases and 33 lineages.

- 19Q2: adds 30 cell lines, 1 primary disease and 1 lineage. This version has different columns than the previous version: the variable "VA_WES_AC" is no longer present in this dataset. Some minor alterations to the original file were made. The first column of the original dataset, (ID, Sample number) was removed, as this column was only the row number and did not serve any unique identifying purpose.

- 19Q3: adds 1 gene, 25 cell lines and removes 1 primary disease.

- 19Q4: adds 1 gene, 10 cell lines, 0 primary diseases and 2 lineages.

- 20Q1: adds 4 genes, 31 cell lines, 1 lineage.

- 20Q2: adds 44 cell lines, 1 lineage.

- 20Q3: no change.

- 20Q4: removes 13 genes, adds 8 cell lines and 1 lineage. Columns 'tumor_sample_barcode' and 'sanger_recalib_WES_AC' were removed.

- 21Q1: removes 11 genes and 2 cell lines.

- 21Q2: removes 1 genes and adds 3 cell lines.

- 21Q3: removes 3 genes, 4 cell lines and 1 lineage.

- 21Q3: removes 3 genes, 4 cell lines and 1 lineage.

- 21Q4: adds 9 cell lines.

- 22Q1: adds 4 cell lines and 1 lineage. The variable 'tumor_seq_allele1' was renamed 'alt_allele'.

- 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_mutationCalls()

## End(Not run)

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