Simulate copy number data for a case-control study.

Share:

Description

Simulate copy number data for a case-control study.

Usage

1
simul(n, nbSNP, probCas, nbSeg, meanSegmentSize, prob, alpha = 15)

Arguments

n

Number of individuals.

nbSNP

Size of the DNA sequence.

probCas

Probability to be a case individual.

nbSeg

Number of causal segments.

meanSegmentSize

The mean size of anormal segment.

prob

A 2*2 matrix containing probabilities:

prob[1,1]=probability to have an anomaly to a SNP given the person does not have the disease and the SNP is causal.

prob[1,2]=probability to have an anomaly to a SNP given the person does not have the disease and the SNP is not causal.

prob[2,1]=probability to have an anomaly to a SNP given the person has the disease and the SNP is causal.

prob[2,2]=probability to have an anomaly to a SNP given the person has the disease and the SNP is not causal.

alpha

Parameter of the beta(alpha,alpha).

Value

a list containing:

data

A matrix of size n*nbSeg, containing values of the copy-number signal.

response

A vector of size n containing the cas/control status.

causalSNP

A vector of size nbSeg containing the center of causal segments.

Author(s)

Quentin Grimonprez, Serge Iovleff

Examples

1
data=simul(50,10000,0.4,10,150,matrix(c(0.1,0.8,0.001,0.001),nrow=2))