falseGrandma | R Documentation |
estimate per-comparison error rates
falseGrandma(
gmaData,
relationship = c("ssGP", "sP"),
llrToTest,
N = 10000,
seed = sample.int(.Machine$integer.max, 1),
itersPerMI = NULL,
errorType = c("falseNegative", "pairwise", "Unrel", "Aunt", "HalfAunt", "ParCous",
"True_GAunt", "True_Unrel", "True_HGAunt", "True_GpCous", "GAunt_Unrel",
"HGAunt_Unrel", "GpCous_Unrel", "GAunt", "GAunt_HGAunt", "Gaunt_GpCous", "HGAunt",
"HGAunt_GpCous", "GpCous"),
MIexcludeProb = 1e-04,
maxMissingGenos = NULL,
method = c("strat", "IS", "test")
)
gmaData |
the gmaData object containing your baseline populations and potential descendents. This
input is created by |
relationship |
the relationship you want to test for: "ssGP" - single sided grandparentage (a pair of either two maternal grandparents OR two paternal grandparents); "sP" - single parent inference |
llrToTest |
a vector of llr thresholds to estimate error rates for |
N |
the number of Monte Carlo samples to take to estimate the error rates (ignored for stratified methods) |
seed |
a positive integer to use as a seed for random number generation. |
errorType |
the type of error estimate to make. Options for relationship = "ssGP": "falseNegative", "Unrel", "True_GAunt", "True_Unrel", "True_HGAunt", "True_GpCous", "GAunt_Unrel", "HGAunt_Unrel", "GpCous_Unrel", "GAunt", "GAunt_HGAunt", "Gaunt_GpCous", "HGAunt", "HGAunt_GpCous", "GpCous". Options for relationship "sP": "falseNegative", "Unrel", "Aunt", "HalfAunt", "ParCous". The "pairwise" option is experimental and should not be used. |
MIexcludeProb |
the maximum probability of exclusion for a true relationship due to
Mendelian incompatibilities. If |
maxMissingGenos |
the maximum number of missing genotypes a sample can have before you would choose to omit it from analysis. Default is 10% of the total number of loci, rounded up |
method |
strat for stratified, IS for importance sampling - currently only available for ssGP. Do not use method = "test", this is currently for internal testing and will be removed. |
itersperMI |
the number of iterations per Mendelian incompatibility, in order of 0, 1, ... (ignored for non-stratified methods) |
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