retrieveGenotypes: Retrieve a matrix of simulated genotypes for a specific set...
In sim1000G: Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes
Description
Usage
Arguments
Examples
Description
Retrieve a matrix of simulated genotypes for a specific set of individual IDs
Usage
1
retrieveGenotypes(ids)
Arguments
ids
Vector of ids of individuals to retrieve.
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
library("sim1000G")
examples_dir = system.file("examples", package = "sim1000G")
vcf_file = file.path(examples_dir, "region.vcf.gz")
vcf = readVCF( vcf_file, maxNumberOfVariants = 100 ,
min_maf = 0.12 ,max_maf = NA)
# For realistic data use the function downloadGeneticMap
generateUniformGeneticMap()
startSimulation(vcf, totalNumberOfIndividuals = 200)
ped1 = newNuclearFamily(1)
retrieveGenotypes(ped1$gtindex)
sim1000G documentation built on June 10, 2019, 1:01 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Examples
Description
Retrieve a matrix of simulated genotypes for a specific set of individual IDs
Usage
1 | retrieveGenotypes(ids)
|
Arguments
ids |
Vector of ids of individuals to retrieve. |
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | library("sim1000G")
examples_dir = system.file("examples", package = "sim1000G")
vcf_file = file.path(examples_dir, "region.vcf.gz")
vcf = readVCF( vcf_file, maxNumberOfVariants = 100 ,
min_maf = 0.12 ,max_maf = NA)
# For realistic data use the function downloadGeneticMap
generateUniformGeneticMap()
startSimulation(vcf, totalNumberOfIndividuals = 200)
ped1 = newNuclearFamily(1)
retrieveGenotypes(ped1$gtindex)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.