deconstructSigs: Identifies Signatures Present in a Tumor Sample

Takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.

AuthorRachel Rosenthal
Date of publication2016-07-29 18:27:06
MaintainerRachel Rosenthal <rachel.rosenthal.14@ucl.ac.uk>
LicenseGPL (>= 2)
Version1.8.0
https://github.com/raerose01/deconstructSigs

View on CRAN

Functions

changeColumnNames Man page
deconstructSigs Man page
deconstructSigs-package Man page
example.output Man page
findSeed Man page
formatContexts Man page
getError Man page
getTriContextFraction Man page
golden.section.search Man page
makePie Man page
mut.to.sigs.input Man page
norm.it Man page
plotSignatures Man page
plotTumor Man page
randomly.generated.tumors Man page
sample.mut.ref Man page
signatures.cosmic Man page
signatures.nature2013 Man page
tri.counts.exome Man page
tri.counts.genome Man page
updateW_GR Man page
vcf.to.sigs.input Man page
whichSignatures Man page

Files

deconstructSigs
deconstructSigs/inst
deconstructSigs/inst/extdata
deconstructSigs/inst/extdata/plotSignatures.png
deconstructSigs/inst/extdata/makePie.png
deconstructSigs/NAMESPACE
deconstructSigs/NEWS
deconstructSigs/data
deconstructSigs/data/example.output.rda
deconstructSigs/data/tri.counts.genome.rda
deconstructSigs/data/tri.counts.exome.rda
deconstructSigs/data/signatures.nature2013.rda
deconstructSigs/data/sample.mut.ref.rda
deconstructSigs/data/signatures.cosmic.rda
deconstructSigs/data/randomly.generated.tumors.rda
deconstructSigs/R
deconstructSigs/R/globalVariables.R deconstructSigs/R/plotting.R deconstructSigs/R/mut.to.sigs.input.R deconstructSigs/R/vcf.to.sigs.input.R deconstructSigs/R/deconstructSigs.R deconstructSigs/R/normalize.data.R deconstructSigs/R/golden_section_search.R deconstructSigs/R/datasets.R deconstructSigs/R/internal.scripts.R deconstructSigs/R/whichSignatures.R
deconstructSigs/README.md
deconstructSigs/MD5
deconstructSigs/DESCRIPTION
deconstructSigs/man
deconstructSigs/man/golden.section.search.Rd deconstructSigs/man/signatures.nature2013.Rd deconstructSigs/man/randomly.generated.tumors.Rd deconstructSigs/man/sample.mut.ref.Rd deconstructSigs/man/plotTumor.Rd deconstructSigs/man/makePie.Rd deconstructSigs/man/getTriContextFraction.Rd deconstructSigs/man/vcf.to.sigs.input.Rd deconstructSigs/man/mut.to.sigs.input.Rd deconstructSigs/man/changeColumnNames.Rd deconstructSigs/man/norm.it.Rd deconstructSigs/man/updateW_GR.Rd deconstructSigs/man/tri.counts.exome.Rd deconstructSigs/man/whichSignatures.Rd deconstructSigs/man/plotSignatures.Rd deconstructSigs/man/getError.Rd deconstructSigs/man/deconstructSigs.Rd deconstructSigs/man/example.output.Rd deconstructSigs/man/findSeed.Rd deconstructSigs/man/tri.counts.genome.Rd deconstructSigs/man/formatContexts.Rd deconstructSigs/man/signatures.cosmic.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.