mc3toGR {BiocOncoTK} | R Documentation

## 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)
         }
      }

[Package BiocOncoTK version 1.7.1 Index]