run.espresso.LD: Runs a full ESPRESSO analysis

In agaye/ESPRESSO.LD: Power Analysis and Sample Size Calculation for two SNPs in Linkage Disequilibrium

Description

This function calls the functions required to run a full ESPRESSO analysis where the model consists of an outcome (binary or continuous) determined by two bi-allelic SNPs that modelled as being in LD

Usage

run.espresso.LD(simulation.params = NULL, pheno.params = NULL,
  geno1.params = NULL, geno2.params = NULL, scenarios2run = 1)

Arguments

simulation.params	general parameters for the scenario(s) to analyse
pheno.params	paramaters for the outcome variables
geno1.params	parameters for the first genetic determinant
geno2.params	parameters for the second genetic determinant
scenarios2run	the indices of the scenarios one wish to analyse

Value

a summary table that contains both the input parameters and the results of the analysis

Author(s)

Gaye A.

References

Montana, G. 2005, HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients., Bioinformatics, vol. 21 (23), pp.4309-4311.

Examples

{

# load the table that hold the input parameters; each of the table
# hold parameters for 4 scenarios:
# scenario 1: a binary outcome determined by two binary SNPs in LD
# scenario 2: a binary outcome determined by two additive SNPs in LD
# scenario 3: a quantitative outcome determined by two binary SNPs in LD
# scenario 4: a quantitative outcome determined by two additive SNPs in LD
data(simulation.params)
data(pheno.params)
data(geno1.params)
data(geno2.params)

# run the function for the first two scenarios, two binomial models
run.espresso.LD(simulation.params, pheno.params, geno1.params, geno2.params, scenarios2run=c(1,2))

# run the function for the last two scenarios, two gaussian models
run.espresso.LD(simulation.params, pheno.params, geno1.params, geno2.params, scenarios2run=c(3,4))

}

agaye/ESPRESSO.LD documentation built on May 10, 2019, 7:31 a.m.