X.pathway_discrete.imbalanced {uni.survival.tree}

Generate a matrix of unbalance gene expressions (discrete version of X.pathway() against to Emura (2012)) in the presence of gene pathways

Description

Generate a matrix of gene expressions in the presence of gene pathways, we first produce the matrix by X.pathway(Emura et al. 2012), then we change each value to 1 ~ 3 depend on the quantile and randomly replace a element to 4 in the last p-(q1+q2) column for each row.

Usage

X.pathway_discrete.imbalanced(n, p, q1, q2, rho1 = 0.5, rho2 = 0.5)

Arguments

n

:the number of individuals (sample size)

p

:the number of genes

q1

:the number of genes in the first pathway

q2

:the number of genes in the second pathway

rho1

:the correlation coefficient for the first pathway

rho2

:the correlation coefficient for the second pathway

Value

X n by p matrix of gene expressions

References

Emura T, Chen YH, Chen HY (2012). Survival Prediction Based on Compound Covariate under Cox Proportional Hazard Models. PLoS ONE 7(10): e47627. doi:10.1371/journal.pone.0047627

Examples

## generate 6 gene expressions from 10 individuals
X.pathway_discrete.imbalanced(n=10,p=6,q1=2,q2=2,rho1=0.5,rho2=0.5)