# Gene-Specific Phenotype EstimatoR

## Documentation for package ‘gespeR’ version 1.31.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.