Release v1.2.5

sigminer 1.2.5

BUG REPORTS

ENHANCEMENTS

• Modified the default visualization of bp_show_survey().
• Enhanced torch check.

NEW FUNCTIONS

• read_sv_as_rs() and sig_tally.RS() for simplified genome rearrangement classification matrix generation (experimental).

DEPRECATED

sigminer 1.2.4

BUG REPORTS

• Fixed the assign problem about match pair in bp_extract_signatures()
  with lpSolve package instead of using my problematic code.

ENHANCEMENTS

• Supported mm10 in read_vcf().
• Removed large data files and store them in Zenodo to reduce package size.
• Added cores check.
• Upgraded SP to v1.1.0 (need test).
• Tried installing Torch before SP (need test).

NEW FUNCTIONS

DEPRECATED

Release v1.2.2

BUG REPORTS

• Fixed bug in silhouette calculation in bp_extract_signatures() (#332).
  PAY ATTENTION: this may affect results.
• Fixed bug using custom signature name in show_sig_profile_loop().

ENHANCEMENTS

• Update SigProfilerExtractor to v1.1.0 (not tested).
• Subset signatures to plot is available by sig_names option.
• sigminer is available in bioconda channel: https://anaconda.org/bioconda/r-sigminer/
• Updated ms strategy in sig_auto_extract() by assigning each signature to its
  best matched reference signatures.
• Added get_shannon_diversity_index() to get diversity index for signatures (#333).
• Added new method "S" (from Steele et al. 2019) for tallying copy number data (#329).
• Included new (RS) reference signatures (related to #331).
• Updated the internal code for getting relative activity in get_sig_exposure().

NEW FUNCTIONS

• bp_get_clustered_sigs() to get clustered mean signatures.

DEPRECATED

Release v1.2.1

Fix CRAN note

Release v1.2.0

BUG REPORTS

ENHANCEMENTS

• A new option cut_p_value is added to show_group_enrichment() to cut continous p values as binned regions.
• A Python backend for sig_extract() is provided.
• User now can directly use sig_extract() and sig_auto_extract() instead of loading NMF package firstly.
• Added benchmark results for different extraction approaches in README.
• The threshold for auto_reduce in sig_fit() is modified from 0.99 to 0.95 and similarity update threshold updated from >0 to >=0.01.
• Removed pConstant option from sig_extract() and sig_estimate(). Now a
  auto-check function is created for avoiding the error from NMF package due to
  no contribution of a component in all samples.

NEW FUNCTIONS

• bp_show_survey2() to plot a simplified version for signature number survey (#330).
• read_xena_variants() to read variant data from UCSC Xena as a MAF object for signature analysis.
• get_sig_rec_similarity() for getting reconstructed profile similarity for Signature object (#293).
• Added functions start with bp_ which are combined to provide a best practice for extracting
  signatures in cancer researches. See more details, run ?bp in your R console.

DEPRECATED

Release v1.1.0

• Added data simulation.
• Suppressed future warnings.
• Fixed p value calculation in bootstrap analysis.
• Fixed typo in show_cor(), thanks to @Miachol.
• Added y_tr option in show_sig_profile() to transform y axis values.
• Optimized default behavior of read_copynumber().
  • Support LOH records when user input minor allele copy number.
  • Set complement = FALSE as default.
  • Free dependencies between option use_all and complement.
• Added visualization support for genome rearrangement signatures (#300).
• Added four database for reference signatures from https://doi.org/10.1038/s43018-020-0027-5 (#299).
• Added new measure 'CV' for show_sig_bootstrap() (#298).
• Added group_enrichment() and show_group_enrichment() (#277).
• Optimized signature profile visualization (#295).
• Updated ?sigminer documentation.
• Added ms strategy to select optimal solution by maximizing cosine similarity
  to reference signatures.
• Added same_size_clustering() for same size clustering.
• Added show_cosmic() to support reading COSMIC signatures in web browser (#288).
• Changed argument rel_threshold behavior in sig_fit() and get_sig_exposure().
  Made them more consistent and allowed un-assigned signature contribution (#285).
• Updated all COSMIC signatures to v3.1 and their aetiologies (#287).

Release v1.0.19

• Added more specific reference signatures from SigProfiler, e.g. SBS_mm9.
• Supported data.frame as input object for sig in get_sig_similarity() and sig_fit().
• Modified g_label option in show_group_distribution() to better control group names.
• Added test option and variable checking in show_cor().
• Updated output_sig() to output signature exposure distribution (#280).
• Added show_cor() for general association analysis.
• Added options in show_group_distribution() to control segments.

v1.0.18

• Fixed bugs when outputing only 1 signatures (related to ShixiangWang/sigflow#17).
• Fixed label inverse bug in add_labels(), thanks to TaoTao for reporting.

v1.0.17

• Handled , seperated indices in show_cosmic_signatures.
• Added option set_order in get_sig_similarity() (#274).
• Outputed more stats information in output_sig().
• Fixed default y axis title in show_sig_bootstrap_error(), now it is "Reconstruction error (L2 norm)"

v1.0.16

• Added auto_reduce option in sig_fit* functions to improve signature fitting.
• Return cosine similarity for sample profile in sig_fit().
• Set default strategy in sig_auto_extract() to 'optimal'.
• Supported search reference signature index in get_sig_cancer_type_index().
• Outputed legacy COSMIC similarity for SBS signatures.
• Added new option in sigprofiler_extract() to reduce failure in when refit is enabled.
• Outputed both relative and absolute signature exposure in output_sig().
• Updated background color in show_group_distribution().
• Modified the default theme for signature profile in COSMIC style.
• Updated the copy number classification method.

v1.0.15

• Handle NULL catalogue.
• Supported ordering the signatures for results from SigProfiler.
• Supported importing refit results from SigProfiler.
• Set optimize option in sig_extract() and sig_auto_extract().