Return catalog row orders for all supported catalog types

Returns a named list containing the canonical row ordering for each catalog type. These are used for validation and ordering of mutation catalogs.

Usage

catalog_row_order()

Value

A named list with elements: SBS96, SBS192, SBS288, SBS1536, DBS78, DBS136, DBS144, ID (83-category COSMIC indels), ID166, ID89, ID476.

Details

Row names use a compact 4-letter format for SBS types: e.g. ACAA encodes the trinucleotide context as <5' base><ref><3' base><alt>. SBS288 row names add a strand prefix: T:ACAA (transcribed), U:ACAA (untranscribed), N:ACAA (non-transcribed).

Examples

cro <- catalog_row_order()
head(cro$SBS96)
#> [1] "ACAA" "ACCA" "ACGA" "ACTA" "CCAA" "CCCA"
length(cro$DBS78)
#> [1] 78