Format
The somatic mutations in the MB study from Parsons et al., broken
down by gene, type (point mutation, amplification,
or deletion), sample,
screen (Discovery or Prevalence),
and, for point mutations, mutation type,
composed of the wild type nucleotide, its context,
and the mutated nucleotide. The object is a data frame,
with the variables: Gene, Type, Sample, Screen, WTNuc
(wild type nucleotide), Context, and MutNuc (mutated
nucleotide). The two possible values
for Screen are Disc ("Discovery") and Prev ("Prevalence").
The three possible values for Type are Mut (point mutations),
Amp (large amplifications), and Del (large deletions.)
Indels have a "" entry for WTNuc, an "All"
entry for Context, and a "ins.del" entry for MutNuc.
Large amplifications and deletions have "" entries for
WTNuc, Context, and MutNuc.