Displaying 2 results from an estimated 2 matches for "readvcf".
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readdcf
2020 Oct 29
1
R: sim1000G
...age to simulate data for case/control study.
I can not figure out how to manipulate this code to be able to generate 10%
or 50% causal SNPs in R.
This is whole code provided as example on GitHub:
library(sim1000G)
vcf_file = "region-chr4-357-ANK2.vcf.gz" #nvariants = 442, ss=1000
vcf = readVCF( vcf_file, maxNumberOfVariants = 442 ,min_maf =
0.0005,max_maf = 0.01) #lowest MAF
dim( vcf$gt1 ) #rows represent number of variants, columns represent
number of individuals
## Download and use full chromosome genetic map
downloadGeneticMap(4)
readGeneticMap(4)
sample.size=3000
startSimulation(...
2020 Nov 01
0
R: sim1000G
...y.
> I can not figure out how to manipulate this code to be able to generate 10%
> or 50% causal SNPs in R.
>
> This is whole code provided as example on GitHub:
>
> library(sim1000G)
> vcf_file = "region-chr4-357-ANK2.vcf.gz" #nvariants = 442, ss=1000
>
> vcf = readVCF( vcf_file, maxNumberOfVariants = 442 ,min_maf =
> 0.0005,max_maf = 0.01) #lowest MAF
> dim( vcf$gt1 ) #rows represent number of variants, columns represent
> number of individuals
>
> ## Download and use full chromosome genetic map
> downloadGeneticMap(4)
> readGeneticMap(4)
&...