simData: Example data: Simulated phenotypes and target relations for 4...

In cbg-ethz/gespeR: Gene-Specific Phenotype EstimatoR

Description

The data set contains simulated data for four screens. Each screen consists of a phenotype vector and target relations between siRNAs and genes, i.e. which siRNA binds which genes (on- and off-targets). The size of each simulated screen is N = 1000 siRNAs x p = 1500 genes. SSPs are generated by first defining GSPs and multiplying the true GSPs with the sampled targe trelation matrices. For sampling the GSPs, we set the number of effect genes to 5 from Normal(0, 3). Target relation matrices are simulated by sampling the number of off-targets per siRNA from Normal(3e-2 * N, 3e-3 * N) and the strength of off-targets is sampled from Beta(2, 5). On-target components are set to 0.75.

Details

The code used to simluate the data can be found in system.file("example", "data_simulation.R", package="gespeR")

Examples

pheno.a <- Phenotypes(system.file("extdata", "Phenotypes_screen_A.txt", package="gespeR"),
type = "SSP", col.id = 1, col.score = 2)
targets.a <- TargetRelations(system.file("extdata", "TR_screen_A.rds", package="gespeR"))

cbg-ethz/gespeR documentation built on May 13, 2019, 2:02 p.m.