COSMIC_hg19_demo: Cosmic coding mutations hg19

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

Description

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

Usage

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.

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