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

View source: R/compare_results.R

compare_cosmic_v3R Documentation

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 July 14, 2024, 8:28 a.m.