Illustration of variant vizualization with TnT

Illustration of variant vizualization with TnT

TnTdemo(
  mae = NULL,
  sitecode = "ACC",
  chr = "11",
  viewstart = 6e+07,
  viewend = 7e+07,
  verbose = TRUE
)

Arguments

mae

instance of MultiAssayExperiment, defaults to NULL

sitecode

character(1) TCGA code, defaults to "ACC"

chr

character(1) chromosome for variant request, defaults to "11"

viewstart

numeric(1) leftmost basepair to view, defaults to 6e7

viewend

numeric(1) rightmost basepair to view, defaults to 7e7

verbose

logical(1) passed to curatedTCGAData::curatedTCGAData

Value

TnT::TnTGenome

Note

Mutation component is extracted from MultiAssayExperiment, and rowRanges method used to obtain addresses of recorded somatic mutations. Non-SNV mutations are dropped.