In Bioconductor/GenomicDataCommons: NIH / NCI Genomic Data Commons Access

Background

Workflow

library(GenomicDataCommons)
library(tibble)

Genes and gene details

grep_fields('genes', 'symbol')

head(available_values('genes','symbol'))

tp53 = genes() |> 
  GenomicDataCommons::filter(symbol=='TP53') |> 
  results(size=10000) |> 
  as_tibble()

ssms

ssms() |> 
    GenomicDataCommons::filter(
      chromosome==paste0('chr',tp53$gene_chromosome[1]) &
        start_position > tp53$gene_start[1] & 
        end_position < tp53$gene_end[1]) |> 
    GenomicDataCommons::count()

ssms() |> 
    GenomicDataCommons::filter(
      consequence.transcript.gene.symbol %in% c('TP53')) |> 
    GenomicDataCommons::count()

convert to VRanges

library(VariantAnnotation)
vars = ssms() |> 
    GenomicDataCommons::filter(
      consequence.transcript.gene.symbol %in% c('TP53')) |> 
    GenomicDataCommons::results_all() |>
    as_tibble()

vr = VRanges(seqnames = vars$chromosome,
             ranges = IRanges(start=vars$start_position, width=1),
             ref = vars$reference_allele,
             alt = vars$tumor_allele)

ssm_occurrences() |> 
    GenomicDataCommons::filter(
      ssm.consequence.transcript.gene.symbol %in% c('TP53')) |>
    GenomicDataCommons::count()

var_samples = ssm_occurrences() |> 
    GenomicDataCommons::filter(
      ssm.consequence.transcript.gene.symbol %in% c('TP53')) |> 
    GenomicDataCommons::expand(c('case', 'ssm', 'case.project')) |>
    GenomicDataCommons::results_all() |> 
    as_tibble()

table(var_samples$case$disease_type)

OncoPrint

fnames <- files() %>%
  GenomicDataCommons::filter(
    cases.project.project_id=='TCGA-SKCM' &
      data_format=='maf' &
      data_type=='Masked Somatic Mutation' &
      analysis.workflow_type ==
        'Aliquot Ensemble Somatic Variant Merging and Masking'
  ) %>%
  results(size = 1) %>%
    ids() %>%
      gdcdata()

library(maftools)
melanoma = read.maf(maf = fnames)

maftools::oncoplot(melanoma)

Bioconductor/GenomicDataCommons documentation built on May 2, 2024, 4:21 p.m.