Compare a result object to COSMIC V2 SBS Signatures (combination whole-exome and whole-genome)

Usage

compare_cosmic_v2(
  musica,
  model_id,
  modality = "SBS96",
  result_name = "result",
  metric = "cosine",
  threshold = 0.9,
  result_rename = deparse(substitute(result)),
  decimals = 2,
  same_scale = FALSE
)

Arguments

musica: A musica object.
model_id: The name of the model containing the signatures to compare.
modality: Compare to SBS, DBS, or Indel. Default "SBS96"
result_name: Name of the result list entry. Default "result".
metric: One of "cosine" for cosine similarity or "jsd" for 1 minus the Jensen-Shannon Divergence. Default "cosine".
threshold: threshold for similarity
result_rename: title for plot user result signatures
decimals: Specifies rounding for similarity metric displayed. Default 2.
same_scale: If TRUE, the scale of the probability for each signature will be the same. If FALSE, then the scale of the y-axis will be adjusted for each signature. Default TRUE.

Value

Returns the comparisons

Examples

data(res)
compare_cosmic_v2(res, model_id = "res", threshold = 0.7)

#>      cosine x_sig_index y_sig_index x_sig_name y_sig_name
#> 4 0.9742418           3           7 Signature3       SBS7
#> 5 0.7730161           3          11 Signature3      SBS11
#> 6 0.7568463           3          30 Signature3      SBS30
#> 1 0.7337470           1          13 Signature1      SBS13
#> 2 0.7296889           2           5 Signature2       SBS5
#> 3 0.7107142           2          19 Signature2      SBS19