simulate_data: Simulate data for robust hirarachical clustering to identify...

In mdbahadur/rhcoclust: Robust Hierarchical Co-Clustering to Identify Significant Co-Cluster

Simulate data for robust hirarachical clustering to identify significant co-cluster

Description

We generate fold change gene expression (FCGE) data according to the characteristics of toxicogenomic data.

Usage

simulate_data(no.gene, no.dcc)

Arguments

no.gene	Number of genes in the simulated data.
no.dcc	Numbe of doses of chemical compounds (dcc) in the simulated data.

Details

There are four gene groups and three DCCs groups in the simulated dataset. The gene group 1, 2, 3 and 4 consists the genes G1-G10, G11-G20, G21-G30 and G31-G50 respectively and DCCs group 1, 2 and 3 consists the DCCs C1_High-C5_High- C1_Middle-C5_Middle, C6_High-C10_High- C6_Middle-C10_Middle and C1_Low-C12_Low- C11_Middle- C12_Middle- C11_High- C12_High respectively. Where, G stands for gene and C stands for chemical compound arranged in the row and column of the simulated data matrix respectively. The error term N(0,0.35) from normal distribution with mean 0 and variance 0.35 is added to each element of the simulated dataset. In the simulated dataset the gene group-1 is up-regulated by the DCCs group-1, gene goup-2 is up and down-regulated by the DCCs group-2 and 1 respectively. The gene group-3 is down-regulated by the DCs group-2. The gene group-4 is not regulated by any of the DCCs groups and DCCs group-3 does not influence any of the genes in the dataset.

Value

A list of object that containing the following:

SimData: A simulated data matrix as generated.

SimDataRnd: Randomly distributed row and column entity of simulated data.

GCmat: Transformed simulated data.

Author(s)

Md. Bahadur Badsha <[e-mail]>

Examples

# Load library
library(rhcoclust)

# Number of genes in the simulated data.
no.gene <- 50

# Numbe of doses of chemical compounds (dcc) in the simulated data.
no.dcc <- 12

SimulteData <- simulate_data(no.gene,no.dcc)

# A simulated data matrix as generated.
SimulteData$SimData

# A randomly distributed row and column entity of simulated data.
SimulteData$SimDataRnd

# A transformed simulated data.
SimulteData$GCmat

mdbahadur/rhcoclust documentation built on Jan. 31, 2023, 10:13 p.m.