Man pages for raerose01/deconstructSigs
Identifies Signatures Present in a Tumor Sample
| changeColumnNames | Re-formats column names |
| dbs_possible | Table of Possible DBS mutations and their reverse complement |
| deconstructSigs | deconstructSigs |
| example.output | Example output of whichSignatures() |
| findSeed | Seeds weight matrix |
| formatContexts | Formats the data for use in plotSignatures() |
| getError | Calculates error |
| getTriContextFraction | Calculates trinucleotide context fraction |
| golden.section.search | Golden section search |
| makePie | Plots the weights from whichSignatures() |
| mut.to.sigs.input | Converts mutation list to correct input format |
| norm.it | Normalizes trinucleotide contexts |
| plotSignatures | Plots the result from whichSignatures() |
| plotTumor | Plots a tumor profile |
| randomly.generated.tumors | Values for 100 randomly generated tumor samples |
| sample.mut.ref | Example input to mut.to.sigs.input() |
| signatures.cosmic | Published Signatures from Sanger COSMIC |
| signatures.dbs.cosmic.v3.may2019 | New DBS Signatures from Sanger COSMIC (May 2019) |
| signatures.exome.cosmic.v3.may2019 | Updated SBS Exome Signatures from Sanger COSMIC (May 2019) |
| signatures.genome.cosmic.v3.may2019 | Updated SBS Genome Signatures from Sanger COSMIC (May 2019) |
| signatures.nature2013 | Published Signatures from Alexandrov et al 2013 |
| tri.counts.exome | The counts of every trinuclotide frequency in an exome |
| tri.counts.genome | The counts of every trinuclotide frequency in a genome |
| updateW_GR | Updates the weights matrix |
| vcf.to.sigs.input | Converts a VCF file to correct input format |
| whichSignatures | Which signatures are present |
