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| LowMACA-package | LowMACA : Low frequency Mutations Analysis via Consensus Alignment |
| alignSequences | Align sequences via clustalo |
| alignSequences-method | Class '"LowMACA"' |
| allPfamAnalysis | Global analysis of a repository of mutations |
| BLOSUM62 | BLOSUM62 matrix |
| bpAll | Draw a mutation barplot |
| bpAll-method | Class '"LowMACA"' |
| entropy | Calculate LowMACA statistics |
| entropy-method | Class '"LowMACA"' |
| getMutations | Retrieve mutation data for a LowMACA object |
| getMutations-method | Class '"LowMACA"' |
| lfm | Show significant clusters of mutations |
| lfm-method | Class '"LowMACA"' |
| lfmSingleSequence | Show significant clusters of mutations of every gene in a LowMACA object without alignment |
| lfmSingleSequence-method | Class '"LowMACA"' |
| lmAlignment | Show Alignment Results from a LowMACA object |
| lmAlignment-method | Class '"LowMACA"' |
| lmEntropy | Show Entropy Information Contained in a LowMACA object |
| lmEntropy-method | Class '"LowMACA"' |
| lmMutations | Show Mutation Data Contained in a LowMACA object |
| lmMutations-method | Class '"LowMACA"' |
| lmObj | Example of a LowMACA object |
| lmParams | Show and set parameters |
| lmParams-method | Class '"LowMACA"' |
| lmParams<- | Show and set parameters |
| lmParams<--method | Class '"LowMACA"' |
| lmPlot | Draw a comprehensive LowMACA plot |
| lmPlot-method | Class '"LowMACA"' |
| lmPlotSingleSequence | Draw a LowMACA comprehensive plot of a specified gene within a LowMACA object |
| lmPlotSingleSequence-method | Class '"LowMACA"' |
| LowMACA | LowMACA : Low frequency Mutations Analysis via Consensus Alignment |
| LowMACA-class | Class '"LowMACA"' |
| LowMACA_AML | Example of a LowMACA object |
| mapMutations | Map mutations on consensus sequence |
| mapMutations-method | Class '"LowMACA"' |
| newLowMACA | Construct a LowMACA object |
| nullProfile | Draw a mutational profile plot |
| nullProfile-method | Class '"LowMACA"' |
| parallelize | Show and set parallelization options |
| parallelize-method | Class '"LowMACA"' |
| parallelize<- | Show and set parallelization options |
| parallelize<--method | Class '"LowMACA"' |
| protter | Draw a Protter plot |
| protter-method | Class '"LowMACA"' |
| setup | Setup of a LowMACA object |
| setup-method | Class '"LowMACA"' |
| show-method | Class '"LowMACA"' |
| showTumorType | List of tumor types |