Package index • mSigSpectra

All functions

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