Man pages for UMCUGenetics/mutSigExtractor
Extracts SNV, indel, DBS, and SV signatures from vcf files.
| assignSigPerMut | Assign a mutational signature to each mutation in a vcf or... |
| cosSim | Cosine similarity |
| DBS_SIGNATURE_PROFILES | DBS signature profiles |
| detSmnvType | Determine SMNV type from REF and ALT |
| extractSigsDbs | Extract doublet substitution signatures |
| extractSigsIndel | Extract indel signatures |
| extractSigsSnv | Extract single nucleotide variant signatures |
| extractSigsSv | Extract structural variant signatures |
| fitToSignatures | Linear least-squares (non-negative) fitting |
| getContextsSv | Determine SV type and length |
| getInfoValues | Get values from INFO field |
| indelSeqFlanksStartEnd | Get the start/end positions for the left/right flanks of an... |
| INDEL_SIGNATURE_PROFILES | Indel signature profiles |
| lsqnonneg | Non-negative least squares fitting |
| nBasesMH | Calculate the number of bases that are homologous to the 3'... |
| nCopiesAlongFlank | Calculate the number of copies of the indel sequence are... |
| plotContexts | Plot contexts |
| readSigsAsDf | Read multiple files outputed my mutSigExtractor into a data... |
| readVcfFields | Read vcf into R as data frame |
| SBS_SIGNATURE_PROFILES_V2 | SBS signature profiles (original 30) |
| SBS_SIGNATURE_PROFILES_V3 | SBS signature profiles (new; v3, May 2019) |
| splitDfRegex | Split data frame or matrix using regex on colnames |
| subsetSmnvs | Subset for SNVs, DBSs, or indels |
| SV_SIGNATURE_PROFILES | SV signature profiles |
| transformContexts | Various transformation of contexts (e.g. into mutational... |
| variantsFromVcf | Extract relevant variant info for extracting SNV, indel, and... |
