v2.3.0

• Supported human T2T genome and corresponding annotation data.
• Updated COSMIC database to v3.4. SV and RNA-SBS signatures are included.

get_sig_db("latest_RNA-SBS_GRCh37")
get_sig_db("latest_SV_GRCh38")

• Fixed a bug in generating matrix for variation categories with strand bias due to problematic counting. (#445)

v2.2.2

Removed sigflow - sigprofiler as the default due to the install issue. If you wanna use the sigprofiler, please previous version or install it with interactive mode.

Release v2.2.1

sigminer 2.2.1

• Fixed the error in generating SBS matrix when only one sample input (#432).

sigminer 2.2.0

• Removed package 'copynumber' from suggests filed.
• Supported Ziyu Tao et al approach for copy number segment classification.
• Supported ce11 genome in read_vcf().
• Added read_maf_minimal() to support a minimal MAF-like data as input.

Release v2.1.3

sigminer 2.1.3

• Fixed error in extracting invalid regions (#396, thanks to @KirsieMin).

sigminer 2.1.2

• Enhanced the read_copynumber_seqz() to include minor copy number. (Thanks to yancey)
• Added input range check in sig_estimate(). (#391)

sigminer 2.1.1

• Expanded output_* function by adding option sig_db.
• Fixed the error using sigminer::get_genome_annotation() before loading it.
• Fixed the bug the get_pLOH_score() return nothing for sample without LOH.

Release 2.1.0

• Added sig_unify_extract() as an unified signature extractor.
• Fixed error showing copy number reference signature profile for CNS_TCGA database.

Release 2.0.5

• Impl y_limits option in show_sig_profile() (#381).
• Added function get_pLOH_score() for representing the genome that displayed LOH.
• Added function read_copynumber_ascat() for reading ASCAT result ASCAT object in .rds format.
• Added function get_intersect_size() for getting overlap size between intervals.
• Added option to get_Aneuploidy_score() to remove short arms of chr13/14/15/21/22 from calculation.

Release 2.0.4

• Implemented Cohen-Sharir method-like Aneuploidy Score.
• Enhanced error handling in show_sig_feature_corrplot() (#376).
• Fixed INDEL classification.
• Fixed end position determination in read_vcf().
• Updated INDEL adjustment.
• Included TCGA copy number signatures from SigProfiler.
• Updated docs.

Release 2.0.1

• Supported mm9 genome build.
• Removed FTP link as CRAN suggested (#359).
• Updated README.

Release 2.0.0

BUG REPORTS

• Fixed the SigProfiler installation error due to Python version in conda environment.
• Fixed classification bug due to repeated function name call_component.
• Fixed the bug when read_vcf() with ## commented VCF files.

ENHANCEMENTS

• Added support for latest COSMIC v3.2 as reference signatures. You can obtain them by

for (i in c("latest_SBS_GRCh37", "latest_DBS_GRCh37", "latest_ID_GRCh37",
            "latest_SBS_GRCh38", "latest_DBS_GRCh38",
            "latest_SBS_mm9", "latest_DBS_mm9",
            "latest_SBS_mm10", "latest_DBS_mm10",
            "latest_SBS_rn6", "latest_DBS_rn6")) {
  message(i)
  get_sig_db(i)
}

• Updated keep_only_pass to FALSE at default.
• Added RSS and unexplained variance calculation in get_sig_rec_similarity().
• Added data check and filter in output_tally() and show_catalogue().
• Enhanced show_group_enrichment() (#353) & added a new option to cluster rows.
• Removed unnecessary CN classifications code in recent development.

NEW FUNCTIONS

DEPRECATED

• Dropped copy number "M"" method to avoid misguiding user to use/read wrong signature profile and keep code simple.

V2 预览版

这是一个预览版本，目前看来基本可以发布，但需要对 sigflow 进行相关测试。