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gespeR (version 1.4.2)

Gene-Specific Phenotype EstimatoR

Description

Estimates gene-specific phenotypes from off-target confounded RNAi screens. The phenotype of each siRNA is modeled based on on-targeted and off-targeted genes, using a regularized linear regression model.

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Version

Version

1.4.2

License

GPL-3

Maintainer

Fabian Schmich

Last Published

February 15th, 2017

Functions in gespeR (1.4.2)

path<-

path
c,Phenotypes-method

Concatenate Phenotypes objects
lasso.rand

Randomized Lasso
plot.concordance

Plot concordance
target.relations

target.relations
gespeR-package

Package: Gene-Specific Phenotype EstimatoR
Phenotypes-class

Phenotypes
stabilityfits

Example fits for phenotypes from simulated screening data A, B, C and D
plot.gespeR

Plot method for gespeR objects
simData

Example data: Simulated phenotypes and target relations for 4 screens (A, B, C, D)
concordance

Evaluate the concordance between Phenotype objects
na.rem

Remove NA/Inf values from phenotype vectors
join

join
as.data.frame.concordance

Coerce method
[,TargetRelations,ANY,ANY,ANY-method

Subsetting for TargetRelations objects.
stability

stability
stability.selection

Stability Selection
scores

scores
loadValues

Methods for values of TargetRelations objects
TargetRelations-class

TargetRelations
annotate.gsp

annotate.gsp
plot.Phenotypes

Plot method for Phenotype objects
[,Phenotypes,ANY,ANY,ANY-method

Subsetting for Phenotype objects.
as.data.frame,Phenotypes-method

Convert Phenotypes object to a data.frame
values

values
dim,Phenotypes-method

Dimension of a Phenotypes object
rbo

Rank biased overlap (Webber et al., 2010)
gsp

Retrieve GSPs and SSPs from gespeR objects
gespeR-class

gespeR