Displaying 3 results from an estimated 3 matches for "data_sim".
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data_size
2006 Aug 26
1
problems with loop
...rn(output)
}
# The negative log likelihood of this model given a data set "new". This
works fine if it is used in the optim() routine with only one data set.
NLL=function(coef)
{
beta0=coef[1]
mu=coef[2]
k=coef[3]
I=coef[4]
data_sim=Model_1(beta0,mu,k,I)
LLsum=0 #log likelihood sum
for (j in 1:length(data_sim[,1]))
{
if (data_sim[j,2]<0 || data_sim[j,3]<0)
{return(1500)}
for (i in 1:length(new[,1]))
{
if (new[...
2020 Oct 29
1
R: sim1000G
...f =
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.value = 0.402
beta.abs = c.value*abs(log10(freq[causal...
2020 Nov 01
0
R: sim1000G
...) #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)
>...