From this comment on #182:

may advise starting with ATRT’s and SMARCB1 deletions

Here, I’m looking at the output of 01-prepare-cn-file.R to see if we recover that information in the segment to gene mapping. The CNVkit SEG file was used for results/annotated_cn.tsv.

`%>%` <- dplyr::`%>%`

Read in data

# read in the output of `01-prepare-cn-file.R`
annotation_cn <- readr::read_tsv(file.path("results", "annotated_cn.tsv"))
Parsed with column specification:
cols(
  gene_symbol = col_character(),
  biospecimen_id = col_character(),
  label = col_character(),
  copy_number = col_double()
)
# read in the clinical file that has the disease type information
histologies_df <- readr::read_tsv(file.path("..", "..", "data", 
                                            "pbta-histologies.tsv"))
Parsed with column specification:
cols(
  .default = col_character(),
  OS_days = col_double(),
  age_last_update_days = col_double(),
  normal_fraction = col_double(),
  tumor_fraction = col_double(),
  tumor_ploidy = col_double()
)
See spec(...) for full column specifications.

Look at copy number information for ATRT

# get ATRT biospecimen identifiers
atrt_specimens <- histologies_df %>%
  dplyr::filter(disease_type_new == "Atypical Teratoid Rhabdoid Tumor") %>%
  dplyr::pull(Kids_First_Biospecimen_ID)
# filter the gene-level CN information to ATRT samples and gene symbols
# containing 'SMARC'
annotation_cn %>%
  dplyr::filter(biospecimen_id %in% atrt_specimens,
                grepl("SMARC", gene_symbol))

Are there any segments that got mapped to SMARCB1 in the file?

sum(annotation_cn$gene_symbol == "SMARCB1")
[1] 0
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