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$gene_end[1]) |> GenomicDataCommons::count()
ssms() |> GenomicDataCommons::filter( consequence.transcript.gene.symbol %in% c('TP53')) |> GenomicDataCommons::count()
library(VariantAnnotation) vars = ssms() |> GenomicDataCommons::filter( consequence.transcript.gene.symbol %in% c('TP53')) |> GenomicDataCommons::results_all() |> as_tibble()
vr = VRanges(seqnames = vars$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()
library(maftools) melanoma = read.maf(maf = fnames)
maftools::oncoplot(melanoma)
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