R Graphical Manual

Last data update: 2014.03.03

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R Release (3.2.3)
CranContrib
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Classification

Results 1 - 10 of 22 found.
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showTumorType (Package: LowMACA) :

Show all the possible tumor types accepted by LowMACA

● Data Source: BioConductor
● Keywords:
● Alias: showTumorType
● 0 images

LowMACA-class (Package: LowMACA) : Class code{"LowMACA"

LowMACA class object describing the properties of mutations mapped on pfam domains or proteins

● Data Source: BioConductor
● Keywords: classes
● Alias: LowMACA-class, alignSequences,LowMACA-method, bpAll,LowMACA-method, entropy,LowMACA-method, getMutations,LowMACA-method, lfm,LowMACA-method, lfmSingleSequence,LowMACA-method, lmAlignment,LowMACA-method, lmEntropy,LowMACA-method, lmMutations,LowMACA-method, lmParams,LowMACA-method, lmParams<-,LowMACA-method, lmPlot,LowMACA-method, lmPlotSingleSequence,LowMACA-method, mapMutations,LowMACA-method, nullProfile,LowMACA-method, parallelize,LowMACA-method, parallelize<-,LowMACA-method, protter,LowMACA-method, setup,LowMACA-method, show,LowMACA-method
● 0 images

LowMACA-package (Package: LowMACA) :

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.

● Data Source: BioConductor
● Keywords: package
● Alias: LowMACA, LowMACA-package
● 0 images

alignSequences (Package: LowMACA) :

Align sequences for an object of class LowMACA

● Data Source: BioConductor
● Keywords:
● Alias: alignSequences
● 0 images

allPfamAnalysis (Package: LowMACA) :

Given a repository of mutations, the method allPfamAnalysis launches the analysis of all the Pfams and single sequences which are involved with at least one mutation.

● Data Source: BioConductor
● Keywords:
● Alias: allPfamAnalysis
● 0 images

bpAll (Package: LowMACA) :

bpAll draws a stacked barplot of the mutations mapped on the consensus sequence

● Data Source: BioConductor
● Keywords:
● Alias: bpAll
● 1 images

entropy (Package: LowMACA) :

entropy is a method for objects of class LowMACA. It calculates global entropy score of the mutation profile of the alignment and a test for every position in the consensus comparing the number of observed mutations against a weigthed random uniform distribution.

● Data Source: BioConductor
● Keywords:
● Alias: entropy
● 0 images

getMutations (Package: LowMACA) :

Exploting the capabilities of the cgdsr package, this method downloads and parse the mutation data of the specified genes in the selected tumor types. It also aggregates and show the frequencies of mutations of every gene in the different tumor types.

● Data Source: BioConductor
● Keywords:
● Alias: getMutations
● 0 images

lfm (Package: LowMACA) :

The method lfm (low frequency mutations) retrieve the original mutations that created the significant clusters calculated with entropy on the consensus

● Data Source: BioConductor
● Keywords:
● Alias: lfm
● 0 images

lfmSingleSequence (Package: LowMACA) :

The method lfmSingleSequence (low frequency mutations in Single Sequence) launch lfm method on every gene or domain inside a LowMACA object without aligning the sequences

● Data Source: BioConductor
● Keywords:
● Alias: lfmSingleSequence
● 0 images