cell_line_ancestry: Cell line ancestry for common cancer cell lines

In seandavi/UCCCReporter: Utilities for University of Colorado Cancer Center reporting

Description

Data are stored at extdata/cancer-cell-lines-ancestry.csv.gz They were accessed on November 15, 2021.

Usage

cell_line_ancestry()

Download

• https://github.com/seandavi/UCCCReporter/raw/main/inst/extdata/cancer-cell-lines-ancestry.csv.gz

Source

http://ecla.moffitt.org/

References

Dutil J, Chen Z, Monteiro AN, Teer JK, Eschrich SA. An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines. Cancer Res. 2019 Apr 1;79(7):1263-1273. doi: 10.1158/0008-5472.CAN-18-2747. Epub 2019 Mar 20. PMID: 30894373; PMCID: PMC6445675.

• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445675/

See Also

Other Data resources: cdc_places(), cdc_social_vulnerability_index(), census_tract_zip_crosswalk(), rural_zips(), zipcode_shapes()

Examples

cl_ancestry = cell_line_ancestry()

head(cl_ancestry)

# Source of cell line
table(cl_ancestry$source)

# cell lines in CCLE?
table(cl_ancestry$ccle_membership)

table(cl_ancestry$ethnicity)

anc_mat = as.matrix(cl_ancestry[,12:18])
heatmap(anc_mat,margins = c(9,1), labRow=NA)

seandavi/UCCCReporter documentation built on Dec. 22, 2021, 11:15 p.m.