snv: Single Nucleotide Variations

In expands: Expanding Ploidy and Allele-Frequency on Nested Subpopulations

Description

Somatic mutations and Loss of Heterozygosity (LOH) of a Glioblastoma tumor (TCGA-06-0152-01).

Usage

data(snv)

Format

Numeric matrix with 773 rows (one per mutation) and 7 columns:
chr - the chromosome
startpos - genomic position
endpos - same as above
REF - ASCII code of the reference nucleotide (in hg18/hg19)
ALT - ASCII code of the B-allele nucleotide
AF_Tumor - allele frequency of B-allele
PN_B - count of B-allele in normal cells. A value of 0 indicates that the mutation has only been detected in the tumor sample (i.e. somatic mutations). A value of 1 indicates that the variant is also present in the normal (control) sample, albeit at reduced allele frequency (i.e. this is a germline variant, which passed the calling filter due to the presence of an LOH event). Other mutations should not be included.

Source

Data derived from The Cancer Genome Atlas (TCGA).

expands documentation built on Sept. 5, 2021, 5:18 p.m.