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LowMACA (version 1.4.2)

LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Description

The LowMACA package is a simple suite of tools to investigate and analyze the mutation profile of several proteins or pfam domains via consensus alignment. You can conduct an hypothesis driven exploratory analysis using our package simply providing a set of genes or pfam domains of your interest.

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Version

Version

1.4.2

License

GPL-3

Maintainer

Stefano de Pretis

Last Published

February 15th, 2017

Functions in LowMACA (1.4.2)

lmPlot

Draw a comprehensive LowMACA plot
LowMACA-class

Class "LowMACA"
lmObj

Example of a LowMACA object
getMutations

Retrieve mutation data for a LowMACA object
bpAll

Draw a mutation barplot
setup

Setup of a LowMACA object
lmAlignment

Show Alignment Results from a LowMACA object
BLOSUM62

BLOSUM62 matrix
nullProfile

Draw a mutational profile plot
lmEntropy

Show Entropy Information Contained in a LowMACA object
showTumorType

List of tumor types
mapMutations

Map mutations on consensus sequence
parallelize

Show and set parallelization options
alignSequences

Align sequences via clustalo
lmPlotSingleSequence

Draw a LowMACA comprehensive plot of a specified gene within a LowMACA object
entropy

Calculate LowMACA statistics
protter

Draw a Protter plot
LowMACA-package

LowMACA : Low frequency Mutations Analysis via Consensus Alignment
lfmSingleSequence

Show significant clusters of mutations of every gene in a LowMACA object without alignment
lmMutations

Show Mutation Data Contained in a LowMACA object
LowMACA_AML

Example of a LowMACA object
allPfamAnalysis

Global analysis of a repository of mutations
lmParams

Show and set parameters
lfm

Show significant clusters of mutations
newLowMACA

Construct a LowMACA object