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sim1000G

R package for simulating genetic marker data.

Author: Apostolos Dimitromanolakis

Maintainer: Apostolos Dimitromanolakis

Installation

The most stable version can be found at CRAN:

install.packages("sim1000G")

Documenation

Documentation and code examples can be found at:

SimulatingFamilyData

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Version

Install

install.packages('sim1000G')

Monthly Downloads

28

Version

1.3

License

GPL (>= 2)

Maintainer

Apostolos Dimitromanolakis

Last Published

August 17th, 2017

Functions in sim1000G (1.3)

downloadGeneticMap

Downloads a genetic map for a particular chromosome under GRCh37 coordinates for use with sim1000G.

generateFakeGeneticMap

Generates a fake genetic map.

Converts centimorgan position to base-pair. Return a list of centimorgan positions that correspond to the bp vector (in basepairs).

newFamily3generations

Generates genotype data for a family of 3 generations

Read a vcf file, with options to filter out low or high frequency markers.

sim1000G-package

Simulations of rare/common variants using haplotype data from 1000 genomes

generateRecombinationDistances

Generate recombination distances using a chi-square model.

generateRecombinationDistances_noInterference

Generate recombination distances using a no-interference model.

Reads a genetic map downloaded from the function downloadGeneticMap.

readGeneticMapFromFile

Reads a genetic map to be used for simulations.

Holds data necessary for a simulation.

computePairIBD1

Computes pairwise IBD1 for a specific pair of individuals. See function computePairIBD12 for description.

plotRegionalGeneticMap

Generates a plot of the genetic map for a specified region.

Utility function that prints a matrix. Useful for IBD12 matrices.

startSimulation

Start the simulation

Writes a plink compatible PED/MAP file from the simulated genotypes

computePairIBD12

Computes pairwise IBD1/2 for a specific pair of individuals

computePairIBD2

Computes pairwise IBD2 for a specific pair of individuals

generateSingleRecombinationVector

Genetates a recombination vector arising from one meiotic event. The origin of segments is coded as (0 - haplotype1 , 1 - haplotype2 )

Holds the genetic map information that is used for simulations.

Creates a regional vcf file using bcftools to extract a region from 1000 genomes vcf files

newFamilyWithOffspring

Simulates genotypes for 1 family with n offspring

newNuclearFamily

Simulates genotypes for 1 family with 1 offspring

crossoverCDFvector

Contains recombination model information.