Genes and gene details

grep_fields('genes', 'symbol')

## [1] "case.follow_ups.molecular_tests.gene_symbol"
## [2] "symbol"

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

## [1] "y_rna"  "actl10" "matr3"  "a1bg"   "a1cf"   "a2m"

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()

## [1] 1498

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

## [1] 1495

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()

## [1] 6594

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)

## 
##                                Acinar Cell Neoplasms 
##                                                   27 
##                         Acute Lymphoblastic Leukemia 
##                                                   22 
##                         Adenomas and Adenocarcinomas 
##                                                 1810 
##                 Adnexal and Skin Appendage Neoplasms 
##                                                    1 
##                                 Basal Cell Neoplasms 
##                                                    1 
##                         Complex Epithelial Neoplasms 
##                                                   16 
##                  Complex Mixed and Stromal Neoplasms 
##                                                   72 
##                Cystic, Mucinous and Serous Neoplasms 
##                                                  625 
##                         Ductal and Lobular Neoplasms 
##                                                  666 
##                            Epithelial Neoplasms, NOS 
##                                                   25 
##                                Fibromatous Neoplasms 
##                                                   12 
##                                  Germ Cell Neoplasms 
##                                                    1 
##                                              Gliomas 
##                                                  670 
## Granular Cell Tumors and Alveolar Soft Part Sarcomas 
##                                                    2 
##                                 Lipomatous Neoplasms 
##                                                    7 
##                                   Lymphoid Leukemias 
##                                                   23 
##                              Mature B-Cell Lymphomas 
##                                                   26 
##                      Mature T- and NK-Cell Lymphomas 
##                                                    5 
##                                Mesothelial Neoplasms 
##                                                   11 
##                            Miscellaneous Bone Tumors 
##                                                    1 
##                            Myelodysplastic Syndromes 
##                                                    3 
##                                    Myeloid Leukemias 
##                                                   32 
##                                  Myomatous Neoplasms 
##                                                   59 
##                                       Neoplasms, NOS 
##                                                  153 
##                                  Nerve Sheath Tumors 
##                                                    1 
##                                   Nevi and Melanomas 
##                                                  119 
##                                         Not Reported 
##                                                  609 
##                  Osseous and Chondromatous Neoplasms 
##                                                   21 
##                                   Plasma Cell Tumors 
##                                                   53 
##                 Soft Tissue Tumors and Sarcomas, NOS 
##                                                   68 
##                        Specialized Gonadal Neoplasms 
##                                                    1 
##                              Squamous Cell Neoplasms 
##                                                 1217 
##                          Thymic Epithelial Neoplasms 
##                                                    4 
##          Transitional Cell Papillomas and Carcinomas 
##                                                  231

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)

## -Reading
## -Validating
## -Silent variants: 211 
## -Summarizing
## --Possible FLAGS among top ten genes:
##   TTN
## -Processing clinical data
## --Missing clinical data
## -Finished in 0.219s elapsed (0.231s cpu)

maftools::oncoplot(melanoma)

## Warning in min(x): no non-missing arguments to min; returning Inf

## Warning in max(x): no non-missing arguments to max; returning -Inf