Compare a result object to COSMIC V3 Signatures; Select exome or genome for SBS and only genome for DBS or Indel classes

Usage

compare_cosmic_v3(
  musica,
  model_id,
  sample_type,
  modality = "SBS96",
  result_name = "result",
  metric = "cosine",
  threshold = 0.9,
  result_rename = deparse(substitute(model_id)),
  decimals = 2,
  same_scale = FALSE
)

Arguments

musica: A musica object.
model_id: The name of the model containing the signatures to compare.
sample_type: exome (SBS only) or genome
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_v3(res,
  model_id = "res", modality = "SBS96",
  sample_type = "genome", threshold = 0.8
)

#>      cosine x_sig_index y_sig_index x_sig_name y_sig_name
#> 2 0.9028629           3           8 Signature3      SBS7b
#> 1 0.8877524           3           7 Signature3      SBS7a