Read PCGR TSV File — pcgr_tiers_tsv

Reads the snvs_indels.tiers.tsv (or v2's snv_indel_ann.tsv.gz) file output by PCGR.

Usage

pcgr_tiers_tsv_read(x = NULL)

Arguments

x: Path to PCGR snvs_indels.tiers.tsv/snv_indel_ann.tsv.gz file.

Value

A tibble with the contents of the input TSV file, or NULL if x is NULL.

Examples

x <- system.file(
  "rawdata/test_data/umccrised/test_sample_WGS/small_variants",
  "TEST-somatic.pcgr.snvs_indels.tiers.tsv",
  package = "RNAsum"
)
(ptsv <- pcgr_tiers_tsv_read(x))
#> # A tibble: 99 × 61
#>    CHROM POS       REF   ALT   GENOMIC_CHANGE    GENOME_VERSION VCF_SAMPLE_ID   
#>    <chr> <chr>     <chr> <chr> <chr>             <chr>          <chr>           
#>  1 3     179218303 G     A     3:g.179218303G>A  grch38         SBJ02999__PRJ22…
#>  2 17    7674894   G     A     17:g.7674894G>A   grch38         SBJ02999__PRJ22…
#>  3 13    110715614 C     G     13:g.110715614C>G grch38         SBJ02999__PRJ22…
#>  4 13    110719444 G     C     13:g.110719444G>C grch38         SBJ02999__PRJ22…
#>  5 8     20250093  C     T     8:g.20250093C>T   grch38         SBJ02999__PRJ22…
#>  6 8     13086457  C     T     8:g.13086457C>T   grch38         SBJ02999__PRJ22…
#>  7 10    31521795  G     C     10:g.31521795G>C  grch38         SBJ02999__PRJ22…
#>  8 9     132927250 G     A     9:g.132927250G>A  grch38         SBJ02999__PRJ22…
#>  9 3     47121452  G     A     3:g.47121452G>A   grch38         SBJ02999__PRJ22…
#> 10 6     117365075 G     C     6:g.117365075G>C  grch38         SBJ02999__PRJ22…
#> # ℹ 89 more rows
#> # ℹ 54 more variables: VARIANT_CLASS <chr>, SYMBOL <chr>, GENE_NAME <chr>,
#> #   CCDS <chr>, CANONICAL <chr>, ENTREZ_ID <chr>, UNIPROT_ID <chr>,
#> #   ENSEMBL_TRANSCRIPT_ID <chr>, ENSEMBL_GENE_ID <chr>, REFSEQ_MRNA <chr>,
#> #   ONCOSCORE <chr>, ONCOGENE <chr>, TUMOR_SUPPRESSOR <chr>,
#> #   ONCOGENE_EVIDENCE <chr>, TUMOR_SUPPRESSOR_EVIDENCE <chr>,
#> #   DISGENET_CUI <chr>, DISGENET_TERMS <chr>, CONSEQUENCE <chr>, …