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

Description Usage Arguments Value Examples

View source: R/compare_results.R

Description

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

Usage

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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

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

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