COSMIC_hg38_demo: Cosmic coding mutations hg38

In acc-bioinfo/TMBleR: Tumor Mutational Burden Quantification From Gene Panels And WES

Description

A dataset containing coding mutations from COSMIC for genome assembly hg38 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.

Usage

COSMIC_hg38_demo

Format

A data frame with 4668373 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

Details

data("COSMIC_hg38_demo") will load the demo dataset as a "COSMIC_hg38 object in the global env

Source

From CosmicCodingMuts.vcf file for hg38 downloaded from https://cancer.sanger.ac.uk/cosmic/download and saved in data-raw as CosmicCodingMuts_hg38.vcf . The dataset was then subset through random stratified sampling to max 10.000 snv per chromosome.

acc-bioinfo/TMBleR documentation built on Dec. 18, 2021, 10:21 p.m.