abf.data.abfreq: ABfreq file example.
Description
Example of ABfreq file: This data is representative of an exome-sequenced tumor sample, e.g. as could be obtained from TCGA.Usage
data(abf.data.abfreq)
Value
- ABfreq is a tab separated text file with column headers. The file has currently 13 columns:
- chromosomewith the chromosome names
- n.basewith the base positions
- base.refwith the base in the reference genome used (usually hg19). Note the
base.ref is NOT the base of the germline. - depth.normalread depth observed in the normal sample
- depth.sampleread depth observed in the tumor sample
- depth.ratioratio of
depth.sample and depth.normal - AfA-allele frequency observed in the tumor sample
- BfB-allele frequency observed in the tumor sample
- ref.zygosityzygosity of the reference sample. "hom" corresponds to AA or BB, whereas "het" corresponds to AB or BA
- GC.percentGC-content (percent), calculated from the reference genome in fixed nucleotide windows
- good.s.readsnumber of reads that passed the quality threshold (threshold specified in the pre-processing software)
- AB.germlinebase found in the germline sample
- AB.samplebase found in the tumor sample