Workflow
library(GenomicDataCommons)
library(tibble)
Genes and gene details
grep_fields('genes', 'symbol')
## [1] "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$gene_end[1]) |>
GenomicDataCommons::count()
## [1] 1345
ssms() |>
GenomicDataCommons::filter(
consequence.transcript.gene.symbol %in% c('TP53')) |>
GenomicDataCommons::count()
## [1] 1341
convert to VRanges
library(VariantAnnotation)
vars = ssms() |>
GenomicDataCommons::filter(
consequence.transcript.gene.symbol %in% c('TP53')) |>
GenomicDataCommons::results_all() |>
as_tibble()
vr = VRanges(seqnames = vars$chromosome,
ranges = IRanges(start=vars$start_position, width=1),
ref = vars$reference_allele,
alt = vars$tumor_allele)
ssm_occurrences() |>
GenomicDataCommons::filter(
ssm.consequence.transcript.gene.symbol %in% c('TP53')) |>
GenomicDataCommons::count()
## [1] 5391
var_samples = ssm_occurrences() |>
GenomicDataCommons::filter(
ssm.consequence.transcript.gene.symbol %in% c('TP53')) |>
GenomicDataCommons::expand(c('case', 'ssm', 'case.project')) |>
GenomicDataCommons::results_all() |>
as_tibble()
table(var_samples$case$disease_type)
##
## Acinar Cell Neoplasms
## 7
## Adenomas and Adenocarcinomas
## 1649
## Adnexal and Skin Appendage Neoplasms
## 1
## Complex Epithelial Neoplasms
## 16
## Complex Mixed and Stromal Neoplasms
## 70
## Cystic, Mucinous and Serous Neoplasms
## 618
## Ductal and Lobular Neoplasms
## 646
## Epithelial Neoplasms, NOS
## 14
## Fibromatous Neoplasms
## 12
## Germ Cell Neoplasms
## 1
## Gliomas
## 499
## Lipomatous Neoplasms
## 6
## Lymphoid Leukemias
## 16
## Mature B-Cell Lymphomas
## 85
## Mesothelial Neoplasms
## 11
## Miscellaneous Bone Tumors
## 1
## Myelodysplastic Syndromes
## 3
## Myeloid Leukemias
## 30
## Myomatous Neoplasms
## 59
## Neoplasms, NOS
## 9
## Nerve Sheath Tumors
## 1
## Nevi and Melanomas
## 91
## Not Reported
## 6
## Osseous and Chondromatous Neoplasms
## 21
## Plasma Cell Tumors
## 53
## Soft Tissue Tumors and Sarcomas, NOS
## 32
## Squamous Cell Neoplasms
## 1204
## Thymic Epithelial Neoplasms
## 4
## Transitional Cell Papillomas and Carcinomas
## 226
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: 197
## -Summarizing
## --Possible FLAGS among top ten genes:
## MUC16
## TTN
## OBSCN
## -Processing clinical data
## --Missing clinical data
## -Finished in 0.389s elapsed (0.360s 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
