PipelineMapping2Parents | R Documentation |
This function is a wrapper for AddAlleleFreqMapping
,
AddGenotypeLikelihood
,
AddGenotypePriorProb_Mapping2Parents
,
AddPloidyChiSq
, and AddGenotypePosteriorProb
.
It covers the full pipeline for estimating genotype posterior probabilities
from read depth in a "RADdata"
object containing data from
a mapping population.
PipelineMapping2Parents(object, n.gen.backcrossing = 0, n.gen.intermating = 0, n.gen.selfing = 0, minLikelihoodRatio = 10, freqAllowedDeviation = 0.05, freqExcludeTaxa = c(GetDonorParent(object), GetRecurrentParent(object), GetBlankTaxa(object)), useLinkage = TRUE, linkageDist = 1e7, minLinkageCorr = 0.5, overdispersion = 9)
object |
A |
n.gen.backcrossing |
An integer, zero or greater, indicating how many generations of backcrossing to the recurrent parent were performed. |
n.gen.intermating |
An integer, zero or greater, indicating how many generations of intermating within the population were performed. |
n.gen.selfing |
An integer, zero or greater, indicating how many generations of selfing were performed. |
minLikelihoodRatio |
The minimum likelihood ratio for determining parental genotypes with
confidence, to be passed to |
freqAllowedDeviation |
For |
freqExcludeTaxa |
A character vector indicating taxa to exclude from allele frequency estimates and ploidy chi-squared estimates. |
useLinkage |
Boolean. Should genotypes at nearby loci (according to genomic alignment data) be used for updating genotype priors? |
linkageDist |
A number, in basepairs, indicating the maximum distance for linked loci.
Ignored if |
minLinkageCorr |
A number ranging from zero to one. Indicates the minimum correlation
coeffienct between weighted mean genotypes at two alleles in order for linkage
data to be used for updating genotype priors. Ignored if
|
overdispersion |
Overdispersion parameter; see |
Unlike IterateHWE
and IteratePopStruct
,
PipelineMapping2Parents
only runs through each function once,
rather than iteratively until convergence.
A "RADdata"
object identical to that passed to the function, with
the following slots added: $alleleFreq
, depthSamplingPermutations
,
$genotypeLikelihood
,
likelyGeno_donor
, likelyGeno_recurrent
, $priorProb
,
$ploidyChiSq
, $posteriorProb
, and if useLinkage = TRUE
,
$alleleLinkages
and $priorProbLD
. See the documentation
for the functions listed in the description for more details on the
data contained in these slots.
Lindsay V. Clark
SetDonorParent
and SetRecurrentParent
to indicate which
individuals are the parents before running the function.
AddGenotypePriorProb_Mapping2Parents
for how ploidy of parents and
progeny is interpreted.
GetWeightedMeanGenotypes
or Export_polymapR
for
exporting genotypes from the resulting object.
StripDown
to remove memory-hogging slots that are no longer
needed after the pipeline has been run.
# load data for the example data(exampleRAD_mapping) # specify donor and recurrent parents exampleRAD_mapping <- SetDonorParent(exampleRAD_mapping, "parent1") exampleRAD_mapping <- SetRecurrentParent(exampleRAD_mapping, "parent2") # run the pipeline exampleRAD_mapping <- PipelineMapping2Parents(exampleRAD_mapping, n.gen.backcrossing = 1) # export results wmgeno <- GetWeightedMeanGenotypes(exampleRAD_mapping)[-(1:2),] wmgeno
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