R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 66 found.
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SCESet-subset (Package: scater) : Subsetting SCESet Objects

Subset method for SCESet objects, which subsets both the expression data, phenotype data, feature data and other slots in the object.

● Data Source: BioConductor
● Keywords:
● Alias: SCESet-subset, [,SCESet,ANY,ANY,ANY-method, [,SCESet,ANY,ANY-method, [,SCESet,ANY-method, [,SCESet-method
● 0 images

SCESet (Package: scater) : The "Single Cell Expression Set" (SCESet) class

S4 class and the main class used by scater to hold single cell expression data. SCESet extends the basic Bioconductor ExpressionSet class.

● Data Source: BioConductor
● Keywords:
● Alias: SCESet, SCESet-class
● 0 images

arrange (Package: scater) : Arrange rows of code{pData(object)

The SCESet returned will have cells ordered by the corresponding variable in pData(object).

● Data Source: BioConductor
● Keywords:
● Alias: arrange, arrange,SCESet-method, arrange.SCESet
● 0 images

bootstraps (Package: scater) : Accessor and replacement for bootstrap results in an SCESet object

SCESet objects can contain an of bootstrap expression values (for example, as generated by the kallisto software for quantifying feature abundance). These functions conveniently access and replace the 'bootstrap' slot with the value supplied, which must be an matrix of the correct size, namely the same number of rows and columns as the SCEset object as a whole.

● Data Source: BioConductor
● Keywords:
● Alias: bootstraps, bootstraps,SCESet-method, bootstraps.SCESet, bootstraps<-, bootstraps<-,SCESet,array-method
● 0 images

calcIsExprs (Package: scater) : Calculate which features are expressed in which cells using a threshold on

Calculate which features are expressed in which cells using a threshold on observed counts, transcripts-per-million, counts-per-million, FPKM, or defined expression levels.

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

calculateFPKM (Package: scater) : Calculate fragments per kilobase of exon per million reads mapped (FPKM)

Calculate fragments per kilobase of exon per million reads mapped (FPKM) values for expression from counts for a set of features.

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

calculateQCMetrics (Package: scater) : Calculate QC metrics

Calculate QC metrics

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

calculateTPM (Package: scater) : Calculate transcripts-per-million (TPM)

Calculate transcripts-per-million (TPM) values for expression from counts for a set of features.

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

cellNames (Package: scater) : Get cell names from an SCESet object

Get cell names from an SCESet object

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

cellPairwiseDistances (Package: scater) : cellPairwiseDistances in an SCESet object

SCESet objects can contain a matrix of pairwise distances between cells. These functions conveniently access and replace the cell pairwise distances with the value supplied, which must be a matrix of the correct size. The function cellDist is simply shorthand for cellPairwiseDistances.

● Data Source: BioConductor
● Keywords:
● Alias: cellDist, cellDist,SCESet-method, cellDist<-, cellDist<-,SCESet,matrix-method, cellDistSCESet, cellPairwiseDistances, cellPairwiseDistances,SCESet-method, cellPairwiseDistances.SCESet, cellPairwiseDistances<-, cellPairwiseDistances<-,SCESet,matrix-method
● 0 images