InterSIM {InterSIM}

InterSIM

Description

This function simulates three inter-related genomic datasets : DNA methylation, gene expression and protein expression.

Usage

InterSIM(n.sample=500, cluster.sample.prop=c(0.30,0.30,0.40), delta.methyl=2.0,
delta.expr=2.0, delta.protein=2.0, p.DMP=0.2,
p.DEG=NULL, p.DEP=NULL, sigma.methyl=NULL, sigma.expr=NULL, sigma.protein=NULL,
cor.methyl.expr=NULL, cor.expr.protein=NULL, do.plot=FALSE, sample.cluster=TRUE,
feature.cluster=TRUE)

Arguments

n.sample

Number of subjects to simulate

cluster.sample.prop

Proportion of samples in the clusters. The number of proportions entered is used to determine the number of clusters in the simulated data. e.g. if (0.3,0.4,0.3) is entered then the number of clusters will be 3.

delta.methyl

Cluster mean shift for methylation data

delta.expr

Cluster mean shift for expression data

delta.protein

Cluster mean shift for protein data

p.DMP

proportion of DE CpGs (DE = Differentially Expressed)

p.DEG

proportion of DE mRNA, if NULL (default) mRNAs mapped by DE CpGs will be selected

p.DEP

proportion of DE protein, if NULL (default) proteins mapped by DE mRNAs will be selected

sigma.methyl

Covariance structure methylation data, if NULL (default) precomputed values will be used. "indep" gives covariance structure with diagonal elements only (Independent features)

sigma.expr

Covariance structure mRNA data, if NULL (default) precomputed values will be used. "indep" gives covariance structure with diagonal elements only (Independent features)

sigma.protein

Covariance structure Protein data, if NULL (default) precomputed values will be used. "indep" gives covariance structure with diagonal elements only (Independent features)

do.plot

TRUE to generate heatmap, default is FALSE

sample.cluster

TRUE (default), if clustering should be done on samples for heatmap. This option will be applicable only if do.plot=TRUE.

feature.cluster

TRUE (default), if clustering should be done on genomic features for heatmap.This option will be applicable only if do.plot=TRUE.

cor.methyl.expr

Correlation between methylation and mRNA, if NULL (default) precomputed values will be used

cor.expr.protein

Correlation between mRNA and protein, if NULL (default) precomputed values will be used

Value

This function returns three datasets as matrices - DNA methylation, gene expression and protein expression. It also returns a vector that has true cluster assignment for each subject in the generated data.

Author(s)

Prabhakar Chalise <[e-mail]>, Rama Raghavan <[e-mail]>, Brooke Fridley <[e-mail]>

Examples

#
prop <- c(0.20,0.30,0.27,0.23)
effect <- 5
sim.data <- InterSIM(n.sample=500, cluster.sample.prop = prop,
delta.methyl=effect, delta.expr=effect, delta.protein=effect,
p.DMP=0.2, p.DEG=NULL, p.DEP=NULL,
sigma.methyl=NULL, sigma.expr=NULL, sigma.protein=NULL,
cor.methyl.expr=NULL, cor.expr.protein=NULL,
do.plot=FALSE, sample.cluster=TRUE, feature.cluster=TRUE)
sim.methyl <- sim.data$dat.methyl
sim.expr <- sim.data$dat.expr
sim.protein <- sim.data$dat.protein