gespeR-class: gespeR

In gespeR: Gene-Specific Phenotype EstimatoR

Description

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.

Usage

gespeR(phenotypes, target.relations, ...)

## S4 method for signature 'Phenotypes,TargetRelations'
gespeR(phenotypes, target.relations,
  mode = c("cv", "stability"), alpha = 0.5, nbootstrap = 100,
  fraction = 0.67, threshold = 0.9, EV = 1, weakness = 0.8,
  ncores = 1, ...)

## S4 method for signature 'numeric,Matrix'
gespeR(phenotypes, target.relations, ...)

Arguments

phenotypes	The siRNA-spefic phenotypes. Single object for univariate phenotypes and list of Phenotypes objects for multivariate phenotypes.
target.relations	The siRNA-to-gene target relations
...	Additional arguments
mode	The mode of covariate selectino ("cv" or "stability")
alpha	The glmnet mixing parameter
nbootstrap	The number of bootstrap samples
fraction	The fraction for each bootstrap sample
threshold	The selection threshold
EV	The expected value of wrongly selected elements
weakness	The weakness parameter for randomised lasso
ncores	The number of cores for parallel computation

Value

A gespeR object

Slots

SSP

The observed siRNA-specific phenotypes

GSP

The deconvoluted gene-specific phenotypes

target.relations

The siRNA-to-gene target relations, e.g. predicted by TargetScan

is.fitted

An indicator wheter the gespeR model was fitted

model

The fitted regularized linear regression model

Author(s)

Fabian Schmich

See Also

gespeR-package

plot.gespeR

gsp

ssp

scores

stability

target.relations

Examples

phenos <- Phenotypes(system.file("extdata", "Phenotypes_screen_A.txt", package = "gespeR"),
type = "SSP",
col.id = 1,
col.score = 2)
trels <- TargetRelations(readRDS(system.file("extdata", "TR_screen_A.rds", package = "gespeR")))
res <- gespeR(phenotypes = phenos,
    target.relations = trels,
    mode = "stability",
    nbootstrap = 100,
    fraction = 0.67,
    threshold = 0.75,
    EV = 1,
    weakness = 0.8,
    ncores = 1)
gsp(res)

gespeR documentation built on Nov. 8, 2020, 5:35 p.m.