Oncotype DX colon cancer recurrence score — oncotype

Computes the Oncotype DX colon cancer recurrence score from the published gene panel. The formula and the panel, including the reference genes, are unchanged from the original calc_oncotypedx_crc() helper.

Usage

oncotype_crc(expression, gene_axis = c("columns", "rows"))

Arguments

expression: Numeric matrix of gene expression values.
gene_axis: Axis that holds the gene symbols. "columns" (the default) expects samples in rows, which is the orientation returned by clean_expression() and the convention inherited from gaofenglib; the two functions therefore compose directly. Use "rows" for matrices with genes in rows and samples in columns.

Value

A tibble with one row per sample: the stromal, cell-cycle, and individual gene scores, the reference score, the corrected scores, the recurrence score, and the recurrence score category ("Low", "Intermediate", or "High").

Examples

panel <- c(
  "BGN", "FAP", "INHBA", "MKI67", "MYC", "MYBL2", "GADD45B",
  "ATP5E", "GPX1", "PGK1", "VDAC2", "UBB"
)
samples_by_genes <- matrix(
  rnorm(3 * 12, 10),
  nrow = 3,
  dimnames = list(paste0("s", 1:3), panel)
)
oncotype_crc(samples_by_genes)
#> # A tibble: 3 × 11
#>   sample stroma cell_cycle individual reference corrected_stroma
#>   <chr>   <dbl>      <dbl>      <dbl>     <dbl>            <dbl>
#> 1 s1       9.66      10.7        8.78      9.80             9.85
#> 2 s2      10.1        9.63       9.53     10.1              9.94
#> 3 s3      10.6       10.7        9.38     10.7              9.91
#> # ℹ 5 more variables: corrected_cell_cycle <dbl>, corrected_individual <dbl>,
#> #   rs_score <dbl>, oncotype_score <dbl>, oncotype_class <fct>

# Genes in rows also work when declared explicitly.
oncotype_crc(t(samples_by_genes), gene_axis = "rows")
#> # A tibble: 3 × 11
#>   sample stroma cell_cycle individual reference corrected_stroma
#>   <chr>   <dbl>      <dbl>      <dbl>     <dbl>            <dbl>
#> 1 s1       9.66      10.7        8.78      9.80             9.85
#> 2 s2      10.1        9.63       9.53     10.1              9.94
#> 3 s3      10.6       10.7        9.38     10.7              9.91
#> # ℹ 5 more variables: corrected_cell_cycle <dbl>, corrected_individual <dbl>,
#> #   rs_score <dbl>, oncotype_score <dbl>, oncotype_class <fct>