# LowMACA - Low frequency Mutation Analysis via Consensus Alignment

## Documentation for package ‘LowMACA’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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