mutSignatures-package |
Decipher Mutational Signatures from Somatic Mutational Catalogs. |
as.data.frame-method |
Convert and/or transpose a mutSignExposures object to data.frame. |
as.data.frame-method |
Convert a mutationCounts object to data.frame. |
as.data.frame-method |
Convert a mutationSignatures object to data.frame. |
as.list-method |
Convert a mutFrameworkParams object to list. |
as.list-method |
Convert a mutationSignatures object to list. |
as.matrix-method |
Convert a mutationCounts object to matrix. |
as.mutation.counts |
Method as.mutation.counts. |
as.mutation.counts-method |
Method as.mutation.counts. |
as.mutation.signatures |
Method as.mutation.signatures. |
as.mutation.signatures-method |
Method as.mutation.signatures. |
as.mutsign.exposures |
Method as.mutsign.exposures. |
as.mutsign.exposures-method |
Method as.mutsign.exposures. |
attachContext |
Attach Nucleotide Context. |
attachMutType |
Attach Mutation Types. |
cbind2 |
Combine two mutationSignatures-class objects. |
cbind2-method |
Combine two mutationSignatures-class objects. |
coerceObj |
Method coerceObj. |
coerceObj-method |
Method coerceObj. |
countMutTypes |
Count Mutation Types. |
decipherMutationalProcesses |
Decipher Mutational Processes Contributing to a Collection of Genomic Mutations. |
extractXvarlinkData |
Extract Variants from XvarlinkData. |
filterSNV |
Filter Single Nucleotide Variants. |
frequencize |
Convert Mutation COunts to PerMille Frequencies. |
getCosmicSignatures |
Obtain COSMIC mutational Signatures. |
getCounts |
Method getCounts. |
getCounts-method |
Method getCounts. |
getFwkParam |
Method getFwkParam. |
getFwkParam-method |
Method getFwkParam. |
getMutationTypes |
Method getMutationTypes. |
getMutationTypes-method |
Method getMutationTypes. |
getSampleIdentifiers |
Method getSampleIdentifiers. |
getSampleIdentifiers-method |
Method getSampleIdentifiers. |
getSignatureIdentifiers |
Method getSignatureIdentifiers. |
getSignatureIdentifiers-method |
Method getSignatureIdentifiers. |
importVCFfiles |
Import Mutation data from VCF files. |
initialize-method |
Class mutFrameworkParams. |
initialize-method |
Class mutSignExposures. |
initialize-method |
Class mutationCounts. |
initialize-method |
Class mutationSignatures. |
matchSignatures |
Match Mutational Signatures. |
msigPlot |
Method msigPlot. |
msigPlot-method |
Method msigPlot. |
mutationCounts-class |
Class mutationCounts. |
mutationSignatures-class |
Class mutationSignatures. |
mutFrameworkParams-class |
Class mutFrameworkParams. |
mutSigData |
Input Data and Examples for Running Mutational Signatures Analyses |
mutSignExposures-class |
Class mutSignExposures. |
plotMutTypeProfile |
Plot Mutation Signature Profiles. |
plotSignExposures |
Plot Signature Exposure Profiles. |
prelimProcessAssess |
Run a Preliminary Process Assess analysis. |
print-method |
Show method of the mutFrameworkParams Class. |
print-method |
Show method of the mutSignExposures Class. |
print-method |
Show method of the mutationCounts Class. |
print-method |
Show method of the mutationSignatures Class. |
processVCFdata |
Process VCF data. |
removeMismatchMut |
Remove Mismatched Mutations. |
resolveMutSignatures |
Resolve Mutation Signatures. |
revCompl |
Compute Reverse Complement sequences. |
setFwkParam |
Method setFwkParam. |
setFwkParam-method |
Method setFwkParam. |
setMutClusterParams |
Set Parameters for Extracting Mutational Signatures. |
show-method |
Show method of the mutFrameworkParams Class. |
show-method |
Show method of the mutSignExposures Class. |
show-method |
Show method of the mutationCounts Class. |
show-method |
Show method of the mutationSignatures Class. |
silhouetteMLB |
Silhouette Analysis. |
simplifySignatures |
Simplify Mutational Signatures. |
sortByMutations |
Sort Data by Mutation Type. |
table2df |
Table Mutation Types by Sample. |
[-method |
Subset a mutSignExposures-class object. |
[-method |
Subset a mutationCounts-class object. |
[-method |
Subset a mutationSignatures-class object. |