optim.relatedness
(Package: DNAtools) :
Estimate theta and the fraction of comparisons between close relatives
Estimates the fraction of comparisons between pairs of close relatives while fitting the theta parameter minimising the object function. The function makes use of the R-package 'Rsolnp' which is an implementation of an solver for non-linear minimisation problems with parameter constraints.
● Data Source:
CranContrib
● Keywords:
● Alias: optim.relatedness
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Prints the summary matrix and possible "big hits".
● Data Source:
CranContrib
● Keywords:
● Alias: print.dbcompare
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dbCollapse
(Package: DNAtools) :
Collapse m/p output to vector
Collapse a m/p-matrix from dbCompare/dbExpect to a vector.
● Data Source:
CranContrib
● Keywords:
● Alias: dbCollapse
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dbExample
(Package: DNAtools) :
Simulated database with 1,000 individuals
Database containing 1,000 simulated DNA profiles typed on ten autosomal markers.
● Data Source:
CranContrib
● Keywords:
● Alias: dbExample
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plot.dbOptim
(Package: DNAtools) :
Plots the fitted object function for estimated familial
Plots the minimised object function for included values of theta
● Data Source:
CranContrib
● Keywords:
● Alias: lines.dbOptim, plot.dbOptim, points.dbOptim
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pContrib
(Package: DNAtools) :
Compute the posterior probabilities for P(m|n0) for a given prior
where m ranges from 1 to code{m.max} and n0 is the observed locus counts.
● Data Source:
CranContrib
● Keywords:
● Alias: pContrib
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noaTabs
(Package: DNAtools) :
Computes the alpha_m variants and their weights.
Computes the alpha_m-vectors and their weights, c(alpha_m), in order to compute the exact distribution of the number of alleles in a m-person DNA mixture.
● Data Source:
CranContrib
● Keywords:
● Alias: noaTabs
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pContrib.locus
(Package: DNAtools) :
Compute the posterior probabilities for P(m|n0) for a given prior P(m)
Compute a matrix of posterior probabilties P(m|n0) where m ranges from 1 to code{m.max}, and n0 is 0,..,code{m.max}. This is done by evaluating P(m|n0)=P(n0|m)P(m)/P(n), where P(n0|m) is evaluated by pNoA.
● Data Source:
CranContrib
● Keywords:
● Alias: pContrib.locus
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print.dbOptim
(Package: DNAtools) :
Prints the results from optim.relatedness()
Prints the evaluated functions for the object function, best estimate of alpha and possibly list of variances.
● Data Source:
CranContrib
● Keywords:
● Alias: print.dbOptim
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freqEst
(Package: DNAtools) :
Simple allele frequency estimation
Estimates allele frequencies from a database with DNA profiles
● Data Source:
CranContrib
● Keywords:
● Alias: freqEst
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