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

In musicatk: Mutational Signature Comprehensive Analysis Toolkit

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))
)

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

Value

Returns the comparisons

Examples

data(res)
compare_cosmic_v3(res, "SBS", "genome", threshold = 0.8)

musicatk documentation built on Nov. 8, 2020, 5:16 p.m.