- catalog
a named numeric vector or a numeric matrix with dimension Nx1.
N is the number of component, 1 is the sample.
- sig
a Signature
object obtained either from sig_extract or sig_auto_extract,
or just a raw signature matrix/data.frame
with row representing components (motifs) and
column representing signatures.
- n
the number of bootstrap replicates.
- sig_index
a vector for signature index. "ALL" for all signatures.
- 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.
- db_type
only used when sig_db
is enabled.
"" for keeping default, "human-exome" for transforming to exome frequency of component,
and "human-genome" for transforming to whole genome frequency of component.
Currently only works for 'SBS'.
- show_index
if TRUE
, show valid indices.
- method
method to solve the minimazation problem.
'NNLS' for non-negative least square; 'QP' for quadratic programming; 'SA' for simulated annealing.
- auto_reduce
if TRUE
, try reducing the input reference signatures to increase
the cosine similarity of reconstructed profile to observed profile.
- SA_not_bootstrap
if TRUE
, directly run 'SA' multiple times with original input instead of
bootstrap samples.
- type
'absolute' for signature exposure and 'relative' for signature relative exposure.
- rel_threshold
numeric vector, a signature with relative exposure
lower than (equal is included, i.e. <=
) this value will be set to 0
(both absolute exposure and relative exposure).
In this case, sum of signature contribution may not equal to 1.
- mode
signature type for plotting, now supports 'copynumber', 'SBS',
'DBS', 'ID' and 'RS' (genome rearrangement signature).
- find_suboptimal
logical, if TRUE
, find suboptimal decomposition with
slightly higher error than the optimal solution by method 'SA'. This is useful
to explore hidden dependencies between signatures. More see reference.
- suboptimal_ref_error
baseline error used for finding suboptimal solution.
if it is NULL
, then use 'SA' method to obtain the optimal error.
- suboptimal_factor
suboptimal factor to get suboptimal error, default is 1.05
,
i.e., suboptimal error is 1.05
times baseline error.
- ...
control parameters passing to argument control
in GenSA
function when use method 'SA'.