sigminer (version 1.2.5)

get_sig_db: 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.

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 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). 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.

See Also

get_sig_similarity, sig_fit and show_cosmic_sig_profile.

Examples

# NOT RUN {
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")
s1
s2
s3
s4
s5
s6
s7
s8
s9
# }