## ----warning=FALSE,message=FALSE---------------------------------------------- library(GenomicDataCommons) library(tibble) ## ----------------------------------------------------------------------------- grep_fields('genes', 'symbol') ## ----------------------------------------------------------------------------- head(available_values('genes','symbol')) ## ----------------------------------------------------------------------------- tp53 = genes() |> GenomicDataCommons::filter(symbol=='TP53') |> results(size=10000) |> as_tibble() ## ----------------------------------------------------------------------------- ssms() |> GenomicDataCommons::filter( chromosome==paste0('chr',tp53$gene_chromosome[1]) & start_position > tp53$gene_start[1] & end_position < tp53$gene_end[1]) |> GenomicDataCommons::count() ## ----------------------------------------------------------------------------- ssms() |> GenomicDataCommons::filter( consequence.transcript.gene.symbol %in% c('TP53')) |> GenomicDataCommons::count() ## ----warning=FALSE,message=FALSE---------------------------------------------- library(VariantAnnotation) vars = ssms() |> GenomicDataCommons::filter( consequence.transcript.gene.symbol %in% c('TP53')) |> GenomicDataCommons::results_all() |> as_tibble() ## ----------------------------------------------------------------------------- vr = VRanges(seqnames = vars$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) ## ----------------------------------------------------------------------------- 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() ## ----cache=TRUE--------------------------------------------------------------- library(maftools) melanoma = read.maf(maf = fnames) ## ----------------------------------------------------------------------------- maftools::oncoplot(melanoma)