Description Usage Arguments Value Examples
View source: R/polyqtlR_functions.R
Function to run the estimate_IBD
function over a range of possible error priors. The function returns
a merged set of results that maximise the marginal likelihood per individual, i.e. allowing a per-individual error rate within the options
provided in the errors argument.
1 |
errors |
Vector of offspring error priors to test (each between 0 and 1) |
... |
Arguments passed to |
A list containing the following components:
maxL_IBD : A nested list as would have been returned by the estimate_IBD function, but composite across error priors to maximise the marginal likelihoods. Note that the $error values per linkage group are now the average error prior across the population per linkage group
MML : A 3d array of the maximal marginal likelihoods, per error prior. Dimensions are individuals, linkage groups, error priors.
error_per_ind : A matrix of the most likely genotyping error rates per individual (in rows) for each linkage group (in columns)
errors : The error priors used (i.e. the input vector is returned for later reference.)
1 2 3 4 5 6 | ## Not run:
data("phased_maplist.4x","SNP_dosages.4x")
maxL_IBD(phased_maplist=phased_maplist.4x,genotypes=SNP_dosages.4x,
ploidy=4,errors=c(0.01,0.02,0.05,0.1))
## End(Not run)
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