search for: startsimulation

Displaying 2 results from an estimated 2 matches for "startsimulation".

2020 Oct 29
1
R: sim1000G
...0 vcf = readVCF( vcf_file, maxNumberOfVariants = 442 ,min_maf = 0.0005,max_maf = 0.01) #lowest MAF dim( vcf$gt1 ) #rows represent number of variants, columns represent number of individuals ## Download and use full chromosome genetic map downloadGeneticMap(4) readGeneticMap(4) sample.size=3000 startSimulation(vcf, totalNumberOfIndividuals = sample.size) data_sim = function(seed.num){ SIM$reset() id = generateUnrelatedIndividuals(sample.size) gt = retrieveGenotypes(id) freq = apply(gt,2,sum)/(2*nrow(gt)) causal = sample(setdiff(1:ncol(gt),which(freq==0)),45) beta.sign = rep(1,45) c.v...
2020 Nov 01
0
R: sim1000G
...2 ,min_maf = > 0.0005,max_maf = 0.01) #lowest MAF > dim( vcf$gt1 ) #rows represent number of variants, columns represent > number of individuals > > ## Download and use full chromosome genetic map > downloadGeneticMap(4) > readGeneticMap(4) > > sample.size=3000 > > startSimulation(vcf, totalNumberOfIndividuals = sample.size) > > data_sim = function(seed.num){ > > SIM$reset() > > id = generateUnrelatedIndividuals(sample.size) > > gt = retrieveGenotypes(id) > > > freq = apply(gt,2,sum)/(2*nrow(gt)) > causal = sample(setdiff(1:ncol(...