compare_cosmic_v3: Compare a result object to COSMIC V3 Signatures; Select exome...

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

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

Description

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
)

campbio/musicatk documentation built on Dec. 25, 2024, 9:34 p.m.