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.
get_sig_db(sig_db = "legacy")
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.
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 |
---|
a list
.
Steele, Christopher D., et al. "Signatures of copy number alterations in human cancer." bioRxiv (2021).
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.
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") s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11