mc3toGR: create a GRanges from the MC3 mutation data

In vjcitn/BiocOncoTK: Bioconductor components for general cancer genomics

create a GRanges from the MC3 mutation data

Description

create a GRanges from the MC3 mutation data

Usage

mc3toGR(
  bq,
  basicfilt = function(data) dplyr::filter(data, Consequence ==
    "non_coding_transcript_exon_variant"),
  maxnrec = 1e+05
)

Arguments

bq	bigrquery BigQueryConnection instance
basicfilt	a dplyr::filter instance or NULL to convert entire MAF
maxnrec	numeric(1) used with dplyr::as.data.frame en route to GRanges

Value

a GRanges instance

Examples

if (interactive()) {
  con = try(pancan_BQ()) # need CGC_BILLING set
  if (!inherits(con, "try-error")) {
     aut = as.character(1:22) # some records in BQ have missing Chromosome
     chk = mc3toGR(con, basicfilt=function(data) dplyr::filter(data,
          project_short_name=="TCGA-BRCA",
          SYMBOL=="TP53", Chromosome %in% aut))
     print(chk[,1:5]) # lots of mcol fields
     table(chk$Variant_Classification)
     }
  }

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