get_stjude_snvs: get St. Jude SNVs

In seandavi/TargetOsteoAnalysis: Access Open-access TARGET Osteosarcoma Data

Description

This function downloads and reads in the "validated SNVs" from the paper "Recurrent Somatic Structural Variations Contribute to Tumorigenesis in Pediatric Osteosarcoma." Cell Reports, April 10, 2014. The paper describes 20 WGS samples and 14 validation osteosarcoma samples analyzed at St Jude.

Usage

get_stjude_snvs()

Value

a tibble of results

References

Chen, Xiang, Armita Bahrami, Alberto Pappo, John Easton, James Dalton, Erin Hedlund, David Ellison, et al. 2014. “Recurrent Somatic Structural Variations Contribute to Tumorigenesis in Pediatric Osteosarcoma.” Cell Reports, April 10, 2014. https://doi.org/10.1016/j.celrep.2014.03.003. Specifically, the data are derived from https://www.cell.com/cms/10.1016/j.celrep.2014.03.003/attachment/281e4b0f-814f-45a0-ae9c-c6fdb812cb8b/mmc4.xlsx

Examples

snvs = get_stjude_snvs()
head(snvs)
colnames(snvs)
head(sort(table(snvs$gene), decreasing=TRUE),20)

seandavi/TargetOsteoAnalysis documentation built on May 22, 2020, 8:23 p.m.