R Graphical Manual

Last data update: 2014.03.03

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Classification

Results 1 - 10 of 29 found.
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Phenotypes-class (Package: gespeR) : Phenotypes

Class used to represent various types of phenotypes, e.g. from siRNA-specific (SSP) or estimated gene-specific phenotypes (GSP).

● Data Source: BioConductor
● Keywords:
● Alias: Phenotypes, Phenotypes,Matrix-method, Phenotypes,cellHTS-method, Phenotypes,character-method, Phenotypes-class
● 0 images

TargetRelations-class (Package: gespeR) : TargetRelations

Class used to represent siRNA-to-gene on- and off-target relations for a knockdown library and a set of genes.

● Data Source: BioConductor
● Keywords:
● Alias: TargetRelations, TargetRelations,Matrix-method, TargetRelations,character-method, TargetRelations-class
● 0 images

annotate.gsp (Package: gespeR) : annotate.gsp

Query Biomart HGNC symbols for the entrez identifiers of estimated GSPs. Currently, only implemented for species "hsapiens".

● Data Source: BioConductor
● Keywords:
● Alias: annotate.gsp, annotate.gsp,Phenotypes-method, annotate.gsp,gespeR-method
● 0 images

as.data.frame,Phenotypes-method (Package: gespeR) : Convert Phenotypes object to a data.frame

Convert Phenotypes object to a data.frame

● Data Source: BioConductor
● Keywords:
● Alias: as.data.frame,Phenotypes-method
● 0 images

as.data.frame.concordance (Package: gespeR) : Coerce method

Coerce method

● Data Source: BioConductor
● Keywords:
● Alias: as.data.frame.concordance
● 0 images

c,Phenotypes-method (Package: gespeR) : Concatenate Phenotypes objects

Concatenate Phenotypes objects

● Data Source: BioConductor
● Keywords:
● Alias: c,Phenotypes-method
● 0 images

concordance (Package: gespeR) : Evaluate the concordance between Phenotype objects

Measures include the correlation (rho) between pairs of phenotypes for the same gene, the rank biased overlap (rbo) of the top and bottom of ranked lists, and the Jaccard index (J) of selected genes.

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

dim,Phenotypes-method (Package: gespeR) : Dimension of a code{linkS4class{Phenotypes

Dimension of a Phenotypes object

● Data Source: BioConductor
● Keywords:
● Alias: dim,Phenotypes-method
● 0 images

gespeR-class (Package: gespeR) : gespeR

Class that represents a gespeR model. It contains a SSP Phenotypes and TargetRelations representing a siRNA knockdown experiment. When the model is fitted, it additionaly contains estimated GSP Phenotypes.

● Data Source: BioConductor
● Keywords:
● Alias: gespeR, gespeR,Phenotypes,TargetRelations-method, gespeR,numeric,Matrix-method, gespeR-class
● 0 images

gespeR-package (Package: gespeR) : Package: Gene-Specific Phenotype EstimatoR

This package provides a model to deconvolute off-target confounded RNAi knockdown phentypes, and methods to investigate concordance between ranked lists of (estimated) phenotypes. The regularized linear regression model can be fitted using two different strategies. (a) Cross-validation over regularization parameters optimising the mean-squared-error of the model and (b) stability selection of covariates (genes) based on a method by Nicolai Meinshausen et al.

● Data Source: BioConductor
● Keywords: package
● Alias: gespeR-package, gespeRpkg
● 4 images