| output_bootstrap {sigminer} | R Documentation |
Output Signature Bootstrap Fitting Results
Description
Output Signature Bootstrap Fitting Results
Usage
output_bootstrap(x, result_dir, mut_type = "SBS", sig_db = mut_type)
Arguments
x |
result from sig_fit_bootstrap_batch. |
result_dir |
a result directory. |
mut_type |
one of 'SBS', 'DBS', 'ID' or 'CN'. |
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 |
Value
Nothing.