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(
  result,
  variant_class,
  sample_type,
  metric = "cosine",
  threshold = 0.9,
  result_name = deparse(substitute(result)),
  decimals = 2,
  same_scale = FALSE
)

Arguments

result	A musica_result object.
variant_class	Compare to SBS, DBS, or Indel
sample_type	exome (SBS only) or genome
metric	One of "cosine" for cosine similarity or "jsd" for 1 minus the Jensen-Shannon Divergence. Default "cosine".
threshold	threshold for similarity
result_name	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, "SBS", "genome", threshold = 0.8)

campbio/musicatk documentation built on May 9, 2024, 2:21 a.m.