stability-methods: stability

In gespeR: Gene-Specific Phenotype EstimatoR

Description

Retrieve a Phenotypes object with stability values from a gespeR object.

Usage

stability(object)

## S4 method for signature 'gespeR'
stability(object)

Arguments

object

A gespeR object

Value

A Phenotypes object of SSPs

Author(s)

Fabian Schmich

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)
stab <- stability(res)
ans <- merge(as.data.frame(gsp(res)), as.data.frame(stability(res)), by = "ID")
colnames(ans)[2:3] <- c("Phenotype", "Stability")
ans[order(ans$Stability, decreasing = TRUE),]

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