Package 'InterSIM'

Simulation of inter-related genomic datasets

Description

InterSIM is an R package that generates three inter-related data set with realistic inter- and intra- relationships based on the DNA methylation, mRNA expression and protein expression from the TCGA ovarian cancer study.

Details

Package:	InterSIM
Type:	Package
Version:	2.2.0
Date:	2018-07-13
License:	GPL>=2

Author(s)

Prabhakar Chalise, Rama Raghavan, Brooke Fridley; Maintainer: Prabhakar Chalise

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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 <[email protected]>, Rama Raghavan <[email protected]>, Brooke Fridley <[email protected]>

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

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