Cosmic coding mutations hg19 — COSMIC_hg19

A dataset containing coding mutations from COSMIC for genome assembly hg19. Since the COSMIC dataset is very large and it requires registration we are bundleing in the package a very small version, just enough to demo the package vignette and test suite. Please refer on the documentation vignette/HOWTO_Import_external_data.html on how to retrieve and use COSMIC data with TMBleR data("COSMIC_hg19_demo") will load the demo dataset as a "COSMIC_hg19 object in the global env

COSMIC_hg19_demo

Format

A data frame with 4740646 rows and 6 variables

CHR: chromosome name, in UCSC format chrN
START: start genomic coordinate, UCSC format
END: start genomic coordinate, UCSC format
STRAND: strand
REF: reference nucleotide
ALT: alternative nucleotide

Source

From CosmicCodingMuts.vcf file for hg19 downloaded from https://cancer.sanger.ac.uk/cosmic/download and saved in data-raw as CosmicCodingMuts_hg19.vcf. The dataset was then subset through random stratified sampling to max 10.000 snv per chromosome.