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 54 found.
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CuffData-class (Package: cummeRbund) : Class "CuffData"

A 'pointer' class for all information (FPKM, annotation, differential expression) for a given feature type (genes, isoforms, TSS, CDS). The methods for this function communicate directly with the SQL backend to present data to the user.

● Data Source: BioConductor
● Keywords: classes
● Alias: CuffData-class, DB,CuffData-method, annotation,CuffData-method, dim,CuffData-method, getFeatures,CuffData-method, makeRnk, makeRnk,CuffData-method
● 0 images

CuffDist-class (Package: cummeRbund) : Class "CuffDist"

A 'pointer' class to information relative to the distribution-level tests (promoters, splicing, and relative CDS usage)

● Data Source: BioConductor
● Keywords: classes
● Alias: CuffDist-class, DB,CuffDist-method, dim,CuffDist-method, samples,CuffDist-method
● 0 images

CuffFeature-class (Package: cummeRbund) : Class "CuffFeature"

A 'data' container class for all FPKM, annotation, and differential expression data for a single feature (gene, isoform, TSS, or CDS).

● Data Source: BioConductor
● Keywords: classes
● Alias: CuffFeature-class, annotation,CuffFeature-method, diffData,CuffFeature-method, fpkmMatrix,CuffFeature-method, length,CuffFeature-method, samples,CuffFeature-method
● 0 images

CuffFeatureSet-class (Package: cummeRbund) : Class "CuffFeatureSet"

A 'data' container class for all FPKM, annotation, and differential expression data for a set of features (genes, isoforms, TSS, CDS).

● Data Source: BioConductor
● Keywords: classes
● Alias: CuffFeatureSet-class, annotation, annotation,CuffFeatureSet-method, diffData,CuffFeatureSet-method, featureNames,CuffFeatureSet-method, features,CuffFeatureSet-method, length,CuffFeatureSet-method, samples,CuffFeatureSet-method
● 0 images

CuffGene-class (Package: cummeRbund) : Class "CuffGene"

A 'data' container class for all FPKM, annotation, and differential expression Data (as well as for all linked features) for a given gene.

● Data Source: BioConductor
● Keywords: classes
● Alias: CDS,CuffGene-method, CuffGene-class, TSS,CuffGene-method, csPie, csPie,CuffGene-method, genePlot, genePlot,CuffGene-method, genes,CuffGene-method, isoforms,CuffGene-method, length,CuffGene-method, makeGeneRegionTrack, makeGeneRegionTrack,CuffGene-method, promoters,CuffGene-method, relCDS,CuffGene-method, splicing,CuffGene-method
● 0 images

CuffGeneSet-class (Package: cummeRbund) : Class "CuffGeneSet"

A 'data' container class for all FPKM, annotation, and differential expression data (an associated features) for a given set of genes.

● Data Source: BioConductor
● Keywords: classes
● Alias: CDS,CuffGeneSet-method, CuffGeneSet-class, TSS,CuffGeneSet-method, genes,CuffGeneSet-method, isoforms,CuffGeneSet-method, promoters,CuffGeneSet-method, relCDS,CuffGeneSet-method, splicing,CuffGeneSet-method
● 0 images

CuffSet-class (Package: cummeRbund) : Class "CuffSet"

A 'pointer' class to connect to, and retrieve data from the SQLite backend database.

● Data Source: BioConductor
● Keywords: classes
● Alias: CuffSet-class
● 0 images

JSdist (Package: cummeRbund) :

JSdist takes a matrix of expression probabilites (calculated directly or output from makeprobs()) and returns a dist object of the pairwise Jensen-Shannon distances between columns

● Data Source: BioConductor
● Keywords: JS, Jensen-Shannon, distance, metric
● Alias: JSdist
● 0 images

JSdistFromP (Package: cummeRbund) :

JSdist takes a matrix of expression probabilites (calculated directly or output from makeprobs()) and returns a matrix of Jensen-Shannon distances between individual rows and a specific vector of probabilities (q)

● Data Source: BioConductor
● Keywords: JS, Jensen-Shannon, distance, metric
● Alias: JSdistFromP
● 0 images

JSdistVec (Package: cummeRbund) :

Returns the Jensen-Shannon Distance (square root of JS divergence) between two probability vectors.

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