ggMutDens: make a ggplot with density traces of mutations per base pair,...

In vjcitn/BiocOncoTK: Bioconductor components for general cancer genomics

make a ggplot with density traces of mutations per base pair, for 'most mutated' tumor types in a given interval

Description

make a ggplot with density traces of mutations per base pair, for 'most mutated' tumor types in a given interval

Usage

ggMutDens(
  bq,
  basicfilt = function(data) dplyr::filter(data, Consequence ==
    "non_coding_transcript_exon_variant"),
  chrname = "15",
  start = 20450000,
  end = 20730000,
  project_volume = 5,
  maxnrec = 50000,
  binwidth = 5000,
  xlab.in = " "
)

Arguments

bq	bigrquery BigQueryConnection instance
basicfilt	a dplyr::filter operation, defaulting to select non-coding variants in mc3 MAF
chrname	character(1) chromosome token in NCBI seqlevels style
start	numeric(1) base coordinate to start
end	numeric(1) base coordinate to end
project_volume	numeric(1) tumor types will have different numbers of contributions; this parameter tells how many tumor types to represent, counting down from the most frequently represented
maxnrec	numeric(1) for as.data.frame
binwidth	numeric(1) passed to geom_freqpoly
xlab.in	character(1) passed to ggplot2::xlab

Value

instance of ggplot

Examples

if (interactive()) {
 if (!requireNamespace("ggplot2")) stop("install ggplot2 to run this function")
 bq = try(pancan_BQ())
 if (!inherits(bq, "try-error")) {
  ggMutDens(bq)
  }
 }

vjcitn/BiocOncoTK documentation built on Feb. 14, 2023, 11:56 p.m.