deconstructSigs: Identifies Signatures Present in a Tumor Sample

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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.

Author
Rachel Rosenthal
Date of publication
2016-07-29 18:27:06
Maintainer
Rachel Rosenthal <rachel.rosenthal.14@ucl.ac.uk>
License
GPL (>= 2)
Version
1.8.0
URLs

View on CRAN

Man pages

changeColumnNames
Re-formats column names
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.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

Files in this package

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