show_cosmic_sig_profile: Plot Reference (Mainly COSMIC) Signature Profile

In sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Plot Reference (Mainly COSMIC) Signature Profile

Description

Plot Reference (Mainly COSMIC) Signature Profile

Usage

show_cosmic_sig_profile(
  sig_index = NULL,
  show_index = TRUE,
  sig_db = "legacy",
  ...
)

Arguments

sig_index	a vector for signature index. "ALL" for all signatures.
show_index	if TRUE, show valid indices.
sig_db	default 'legacy', it can be 'legacy' (for COSMIC v2 'SBS'), 'SBS', 'DBS', 'ID' and 'TSB' (for COSMIV v3.1 signatures) for small scale mutations. For more specific details, it can also be 'SBS_hg19', 'SBS_hg38', 'SBS_mm9', 'SBS_mm10', 'DBS_hg19', 'DBS_hg38', 'DBS_mm9', 'DBS_mm10' to use COSMIC v3 reference signatures from Alexandrov, Ludmil B., et al. (2020) (reference #1). In addition, it can be one of "SBS_Nik_lab_Organ", "RS_Nik_lab_Organ", "SBS_Nik_lab", "RS_Nik_lab" to refer reference signatures from Degasperi, Andrea, et al. (2020) (reference #2); "RS_BRCA560", "RS_USARC" to reference signatures from BRCA560 and USARC cohorts; "CNS_USARC" (40 categories), "CNS_TCGA" (48 categories) to reference copy number signatures from USARC cohort and TCGA; "CNS_TCGA176" (176 categories) and "CNS_PCAWG176" (176 categories) to reference copy number signatures from PCAWG and TCGA separately. UPDATE, the latest version of reference version can be automatically downloaded and loaded from https://cancer.sanger.ac.uk/signatures/downloads/ when a option with latest_ prefix is specified (e.g. "latest_SBS_GRCh37"). Note: the signature profile for different genome builds are basically same. And specific database (e.g. 'SBS_mm10') contains less signatures than all COSMIC signatures (because some signatures are not detected from Alexandrov, Ludmil B., et al. (2020)). For all available options, check the parameter setting.
...	other arguments passing to show_sig_profile.

Value

a ggplot object

Author(s)

Shixiang Wang [e-mail]

Examples

show_cosmic_sig_profile()
show_cosmic_sig_profile(sig_db = "SBS")
show_cosmic_sig_profile(sig_index = 1:5)
show_cosmic_sig_profile(sig_db = "SBS", sig_index = c("10a", "17a"))

gg <- show_cosmic_sig_profile(sig_index = 1:5)
gg$aetiology

sigminer documentation built on May 29, 2024, 3:11 a.m.