Gene-Specific Phenotype EstimatoR


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Documentation for package ‘gespeR’ version 1.16.0

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gespeR-package Package: Gene-Specific Phenotype EstimatoR
annotate.gsp annotate.gsp
annotate.gsp-method annotate.gsp
as.data.frame-method Convert Phenotypes object to a data.frame
as.data.frame.concordance Coerce method
c-method Concatenate Phenotypes objects
concordance Evaluate the concordance between Phenotype objects
dim-method Dimension of a 'Phenotypes' object
gespeR gespeR
gespeR-class gespeR
gespeR-method gespeR
gespeRpkg Package: Gene-Specific Phenotype EstimatoR
gsp Retrieve GSPs and SSPs from 'gespeR' objects
gsp-method Retrieve GSPs and SSPs from 'gespeR' objects
join join
join-method join
lasso.rand Randomized Lasso
loadValues Methods for values of 'TargetRelations' objects
loadValues-method Methods for values of 'TargetRelations' objects
na.rem Remove NA/Inf values from phenotype vectors
na.rem-method Remove NA/Inf values from phenotype vectors
path<- path
path<--method path
Phenotypes Phenotypes
Phenotypes-class Phenotypes
Phenotypes-method Phenotypes
plot.concordance Plot concordance
plot.gespeR Plot method for 'gespeR' objects
plot.Phenotypes Plot method for Phenotype objects
rbo Rank biased overlap (Webber et al., 2010)
scores scores
scores-method scores
simData Example data: Simulated phenotypes and target relations for 4 screens (A, B, C, D)
ssp Retrieve GSPs and SSPs from 'gespeR' objects
ssp-method Retrieve GSPs and SSPs from 'gespeR' objects
stability stability
stability-method stability
stability.selection Stability Selection
stabilityfits Example fits for phenotypes from simulated screening data A, B, C and D
target.relations target.relations
target.relations-method target.relations
TargetRelations TargetRelations
TargetRelations-class TargetRelations
TargetRelations-method TargetRelations
unloadValues Methods for values of 'TargetRelations' objects
unloadValues-method Methods for values of 'TargetRelations' objects
values values
values-method values
writeValues Methods for values of 'TargetRelations' objects
writeValues-method Methods for values of 'TargetRelations' objects
[-method Subsetting for Phenotype objects.
[-method Subsetting for TargetRelations objects.