Package: mSigSpectra 0.1.3

mSigSpectra: Build Mutational-Spectrum Catalogs from Variant Call Format Files

Reads variant call format (VCF) files in a caller-agnostic way, annotates variants with flanking sequence context and transcriptional strand, and builds mutational-spectrum catalogs of single base substitutions (SBS), doublet base substitutions (DBS), and small insertions and deletions (indels, ID) at several resolutions (SBS96, SBS192, SBS1536, DBS78, DBS136, DBS144, ID83, ID89, ID166, ID476) and in both counts and density representations. Successor to the numerical core of the 'ICAMS' package with plotting, 'shiny', and portable document format (PDF) reporting removed; plotting is provided separately by 'mSigPlot'. Used in the preparation of Rozen et al. (2026) <doi:10.5281/zenodo.18451842>.

Authors:Steve Rozen [aut, cre], Nanhai Jiang [aut], Arnoud Boot [aut], Mo Liu [aut], Yang Wu [aut], Mi Ni Huang [aut], Jia Geng Chang [aut]

# Install 'mSigSpectra' in R:

install.packages('mSigSpectra', repos = c('https://steverozen.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/steverozen/msigspectra/issues

Pkgdown/docs site:https://steverozen.github.io

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

all.abundance - K-mer abundances for density calculations
trans.ranges.GRCh37 - Transcript ranges for transcriptional strand annotation
trans.ranges.GRCh38 - Transcript ranges for transcriptional strand annotation
trans.ranges.GRCm38 - Transcript ranges for transcriptional strand annotation

On CRAN:

cpp

4.80 score 14 scripts 660 downloads 32 exports 47 dependencies

Last updated from:1848df872c. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	317
linux-devel-x86_64	OK	391
source / vignettes	OK	396
linux-release-arm64	OK	301
linux-release-x86_64	OK	412
macos-release-arm64	OK	392
macos-release-x86_64	OK	449
macos-oldrel-arm64	OK	347
macos-oldrel-x86_64	OK	447
windows-devel-arm64	OK	428
windows-devel-x86_64	OK	424
windows-release-arm64	OK	432
windows-release-x86_64	OK	342
windows-oldrel-x86_64	OK	365
wasm-release	OK	198

Exports:add_seq_context add_transcript_strand annot_vcf_to_476_catalog annot_vcf_to_83_catalog annot_vcf_to_89_catalog annotate_id_vcf annotate_sbs_or_dbs_vcf as_catalog catalog_attrs catalog_row_order categorize_1_justified_indel cbind_catalogs change_476_type_ids_to_open_intervals change_89_type_ids_to_open_intervals check_and_remove_discarded_variants collapse_catalog infer_trans_ranges is_catalog justify_id_vcf justify_indel read_catalog read_vcf read_vcfs seg_simple segment_simple_cpp split_vcf subset_catalog transform_catalog vcf_to_dbs_catalog vcf_to_id_catalog vcf_to_sbs_catalog write_catalog

Dependencies:askpass BH BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome cigarillo codetools cpp11 crayon curl data.table fastrc formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r matrixStats mime openssl R6 Rcpp RCurl restfulr Rhtslib rjson Rsamtools rtracklayer S4Vectors Seqinfo snow stringi sys UCSC.utils XML XVector yaml

Reading VCFs and Building Mutational-Spectrum Catalogs

Rendered frommSigSpectra.Rmdusingknitr::rmarkdown

Last update: 2026-05-07
Started: 2026-04-21

Help page	Topics
Add flanking sequence context to a VCF data frame	add_seq_context
Annotate a VCF data frame with transcript strand information	add_transcript_strand
K-mer abundances for density calculations	all.abundance
Convert an annotated indel VCF to a Koh 476-category catalog	annot_vcf_to_476_catalog
Convert an annotated indel VCF to a COSMIC 83-category catalog	annot_vcf_to_83_catalog
Convert an annotated indel VCF to a Koh 89-category catalog	annot_vcf_to_89_catalog
Annotate an in-memory ID (indel) VCF with sequence context, transcript strand, and COSMIC / Koh indel categories	annotate_id_vcf
Annotate an SBS or DBS VCF with flanking sequence context and transcript strand	annotate_sbs_or_dbs_vcf
Turn a numeric matrix into a mutational-spectrum catalog	as_catalog
Report the attributes of an mSigSpectra catalog	catalog_attrs
Return catalog row orders for all supported catalog types	catalog_row_order
Given a indel and its sequence context, categorize it	categorize_1_justified_indel
Combine catalogs across samples (column-bind)	cbind_catalogs
Change 476-type indel category identifiers to use right-open repeat intervals	change_476_type_ids_to_open_intervals
Change 89-type indel category identifiers to use right-open repeat intervals	change_89_type_ids_to_open_intervals
Check a VCF for common variant-level problems and remove the offenders	check_and_remove_discarded_variants
Collapse a higher-resolution catalog to a lower-resolution one	collapse_catalog
Infer transcript ranges for a reference genome	infer_trans_ranges
Check whether an object looks like an mSigSpectra catalog	is_catalog
Add sequence context and transcript information to an in-memory ID (insertion/deletion) VCF, and confirm that they match the given reference genome	justify_id_vcf
Move the notional position of a deletion or insertion as far left as possible.	justify_indel
Read a mutational-spectrum catalog from a file	read_catalog
Read a VCF file into a data.table, caller-agnostically	read_vcf
Read multiple VCF files	read_vcfs
Segment a single indel sequence using Rcpp interface	seg_simple
Segment a single indel using Rcpp interface	segment_simple_cpp
Split a mixed-mutation VCF into SBS / DBS / ID sub-tables	split_vcf
Subset a catalog while preserving attributes	subset_catalog
Transcript ranges for transcriptional strand annotation	trans.ranges trans.ranges.GRCh37 trans.ranges.GRCh38 trans.ranges.GRCm38
Transform a catalog between counts and density	transform_catalog
Build a DBS mutational-spectrum catalog from an annotated DBS VCF	vcf_to_dbs_catalog
Build an ID (indel) mutational-spectrum catalog from an annotated ID VCF	vcf_to_id_catalog
Build an SBS mutational-spectrum catalog from an annotated SBS VCF	vcf_to_sbs_catalog
Write a mutational-spectrum catalog to a file	write_catalog

Package: mSigSpectra 0.1.3

mSigSpectra: Build Mutational-Spectrum Catalogs from Variant Call Format Files

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