get_sig_db: Get Curated Reference Signature Database

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

Get Curated Reference Signature Database

Description

Reference mutational signatures and their aetiologies, mainly obtained from COSMIC database (SigProfiler results) and cleaned before saving into sigminer package. You can obtain:

• COSMIC legacy SBS signatures.

• COSMIC v3 SBS signatures.

• COSMIC v3 DBS signatures.

• COSMIC v3 ID (indel) signatures.

• SBS and RS (rearrangement) signatures from Nik lab 2020 Nature Cancer paper.

• RS signatures from BRCA560 and USARC cohorts.

• Copy number signatures from USARC cohort and TCGA.

• Copy number signatures from Liu lab 2023. It supports both PCAWG and TCGA cohort.

Usage

get_sig_db(sig_db = "legacy")

Arguments

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.

Value

a list.

References

• Steele, Christopher D., et al. "Signatures of copy number alterations in human cancer." Nature 606.7916 (2022): 984-991.

• Alexandrov, Ludmil B., et al. "The repertoire of mutational signatures in human cancer." Nature 578.7793 (2020): 94-101.

• Steele, Christopher D., et al. "Undifferentiated sarcomas develop through distinct evolutionary pathways." Cancer Cell 35.3 (2019): 441-456.

• Ziyu Tao, et al. "The repertoire of copy number alteration signatures in human cancer." Briefings in Bioinformatics (2023): bbad053.

See Also

get_sig_similarity, sig_fit and show_cosmic_sig_profile.

Examples

s1 <- get_sig_db()
s2 <- get_sig_db("SBS")
s3 <- get_sig_db("DBS")
s4 <- get_sig_db("DBS_mm10")
s5 <- get_sig_db("SBS_Nik_lab")
s6 <- get_sig_db("ID")
s7 <- get_sig_db("RS_BRCA560")
s8 <- get_sig_db("RS_USARC")
s9 <- get_sig_db("RS_Nik_lab")
s10 <- get_sig_db("CNS_USARC")
s11 <- get_sig_db("CNS_TCGA")
s12 <- get_sig_db("CNS_TCGA176")
s13 <- get_sig_db("CNS_PCAWG176")
s1
s2
s3
s4
s5
s6
s7
s8
s9
s10
s11
s12
s13

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