1 Background

2 Workflow

library(GenomicDataCommons)
library(tibble)

2.1 Genes and gene details

grep_fields('genes', 'symbol')
## [1] "symbol"
head(available_values('genes','symbol'))
## [1] "y_rna"  "ccdc39" "matr3"  "a1bg"   "a1cf"   "a2m"
tp53 = genes() %>% 
  GenomicDataCommons::filter(symbol=='TP53') %>% 
  results(size=10000) %>% 
  as_tibble()

2.2 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] 1290
ssms() %>% 
    GenomicDataCommons::filter(
      consequence.transcript.gene.symbol %in% c('TP53')) %>% 
    GenomicDataCommons::count()
## [1] 1288

2.3 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] 5030
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 
##                                           7 
##                Adenomas and Adenocarcinomas 
##                                        1467 
##        Adnexal and Skin Appendage Neoplasms 
##                                           1 
##                Complex Epithelial Neoplasms 
##                                          16 
##         Complex Mixed and Stromal Neoplasms 
##                                          69 
##       Cystic, Mucinous and Serous Neoplasms 
##                                         630 
##                Ductal and Lobular Neoplasms 
##                                         616 
##                   Epithelial Neoplasms, NOS 
##                                           9 
##                       Fibromatous Neoplasms 
##                                          12 
##                         Germ Cell Neoplasms 
##                                           1 
##                                     Gliomas 
##                                         483 
##                        Lipomatous Neoplasms 
##                                           6 
##                          Lymphoid Leukemias 
##                                           2 
##                     Mature B-Cell Lymphomas 
##                                           5 
##                       Mesothelial Neoplasms 
##                                          11 
##                   Miscellaneous Bone Tumors 
##                                           1 
##                           Myeloid Leukemias 
##                                          10 
##                         Myomatous Neoplasms 
##                                          59 
##                         Nerve Sheath Tumors 
##                                           1 
##                          Nevi and Melanomas 
##                                          85 
##                                Not Reported 
##                                           9 
##                          Plasma Cell Tumors 
##                                          60 
##        Soft Tissue Tumors and Sarcomas, NOS 
##                                          32 
##                     Squamous Cell Neoplasms 
##                                        1208 
##                 Thymic Epithelial Neoplasms 
##                                           4 
## Transitional Cell Papillomas and Carcinomas 
##                                         226

2.4 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 = 6) %>%
    ids() %>% 
      gdcdata()
library(maftools)
melanoma = read.maf(maf = fnames[2])
## -Reading
## -Validating
## -Silent variants: 200 
## -Summarizing
## -Processing clinical data
## --Missing clinical data
## -Finished in 1.213s elapsed (1.229s 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