computePairIBD1: Computes pairwise IBD1 for a specific pair of individuals....
In adimitromanolakis/sim1000G: Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes
Description
Usage
Arguments
Value
Examples
Description
Computes pairwise IBD1 for a specific pair of individuals.
See function computePairIBD12 for description.
Usage
1
computePairIBD1(i, j)
Arguments
i
Index of first individual
j
Index of second individual
Value
Mean IBD1 as computed from shared haplotypes
Examples
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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)
v = computePairIBD1(1, 3)
cat("IBD1 of pair = ", v, "\n");
adimitromanolakis/sim1000G documentation built on Sept. 29, 2021, 3:44 a.m.
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Description Usage Arguments Value Examples
Description
Computes pairwise IBD1 for a specific pair of individuals. See function computePairIBD12 for description.
Usage
1 | computePairIBD1(i, j)
|
Arguments
i |
Index of first individual |
j |
Index of second individual |
Value
Mean IBD1 as computed from shared haplotypes
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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)
v = computePairIBD1(1, 3)
cat("IBD1 of pair = ", v, "\n");
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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