snv: Single Nucleotide Variations

Description Usage Format Source


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




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.


Data derived from The Cancer Genome Atlas (TCGA).

noemiandor/expands documentation built on July 2, 2018, 4:17 a.m.