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Returns counts of the number of markers at which a pair of subjects shares 0, 1 or 2 alleles identical-by-state (IBS), for all possible pairs. Counts for a given pair exclude markers where either pair member is missing data.
● Data Source:
CranContrib
● Keywords: univar
● Alias: countIBS
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IBDcheck
(Package: CrypticIBDcheck) :
estimate IBD coefficients to identify cryptic relatedness in genetic association studies
Estimate IBD coefficients for pairs of study subjects. Optionally, IBD coefficients are estimated from simulated unrelated, monozygotic twin/duplicate, parent-offspring, full sibling, half sibling, or cousin pairs. Users may also specify their own relationships to simulate (see Examples). Simulations can make use of information about population linkage disequilibrium structure. The function returns an object of class IBD that can be graphically displayed by the plot method of the class, plot.IBD.
● Data Source:
CranContrib
● Keywords: univar
● Alias: IBDcheck
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new.IBD
(Package: CrypticIBDcheck) :
Create a data structure suitable for input to code{IBDcheck
Create a data structure suitable for input to IBDcheck. This is a wrapper function for the constructor function IBD that creates the object. The wrapper provides basic checks of the input and creates the snp.support and subject.support data frames required for an IBD object.
● Data Source:
CranContrib
● Keywords:
● Alias: new.IBD
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Interactive graphical display of an IBD object.
● Data Source:
CranContrib
● Keywords: hplot
● Alias: plot.IBD
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filter.control
(Package: CrypticIBDcheck) :
Set options for quality control filtering of data.
Set options for quality control filtering of data.
● Data Source:
CranContrib
● Keywords:
● Alias: filter.control
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Convert physical map positions on build 36 of the genome to genetic map positions by linear interpolation of the Rutgers combined linkage-physical map. The markers in the Rutgers map are a small subset of markers for which genetic map positions have been determined. Linear interpolation is done for points in between.
● Data Source:
CranContrib
● Keywords:
● Alias: SNPgenmap
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sim.control
(Package: CrypticIBDcheck) :
Set options that control gene drop simulation of relationship pairs.
Set options that control gene drop simulation of relationship pairs.
● Data Source:
CranContrib
● Keywords:
● Alias: sim.control
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IBD
(Package: CrypticIBDcheck) :
Constructor function for objects of class code{IBD
Constructor function for objects of class IBD, used as both the input and output of the IBDcheck function. This is not intended to be called by users. Users preparing data for a call to IBDcheck should use the wrapper function new.IBD, which provides basic checks of the input.
● Data Source:
CranContrib
● Keywords:
● Alias: IBD, IBD-class
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CrypticIBDcheck can be used to identify pairs of closely-related subjects based on genetic marker data from single-nucleotide polymorphisms (SNPs). The package is able to accommodate SNPs in linkage disequibrium (LD), without the need to thin the markers so that they are approximately independent in the population. Sample pairs are identified as related by superposing their estimated identity-by-descent (IBD) coefficients on plots of IBD coefficients for pairs of simulated subjects from one of several common close relationships. The methods are particularly relevant to candidate-gene association studies, in which dependent SNPs cluster in a relatively small number of genes spread throughout the genome.
● Data Source:
CranContrib
● Keywords: package
● Alias: CrypticIBDcheck, CrypticIBDcheck-package
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