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Example output from pedigree inference: 'HSg5'

SeqOUT_HSg5.Rd

Example output of a sequoia run including sibship clustering, based on Pedigree Geno_HSg5.

Usage

data(SeqOUT_HSg5)

Format

a list, see sequoia

See also

Ped_HSg5, LH_HSg5

Author

Jisca Huisman, jisca.huisman@gmail.com

Examples

if (FALSE) {
# this output was created as follows:
Geno <- SimGeno(Ped = Ped_HSg5, nSnp = 200)
SeqOUT_HSg5 <- sequoia(GenoM = Geno, LifeHistData = LH_HSg5, Module = "ped",
                       Err = 0.005)
}
# some ways to inspect the output; see vignette for more info:
names(SeqOUT_HSg5)
#>  [1] "Specs"            "ErrM"             "args.AP"          "Snps-LowCallRate"
#>  [5] "AgePriors"        "LifeHist"         "DupLifeHistID"    "NoLH"            
#>  [9] "PedigreePar"      "TotLikPar"        "LifeHistPar"      "Pedigree"        
#> [13] "DummyIDs"         "TotLikSib"        "AgePriorExtra"    "LifeHistSib"     
SeqOUT_HSg5$Specs
#>       NumberIndivGenotyped NumberSnps GenotypingErrorRate MaxMismatchDUP
#> Specs                  920        200               0.005             11
#>       MaxMismatchOH MaxMismatchME Tfilter Tassign nAgeClasses MaxSibshipSize
#> Specs             5             8      -2     0.5           6            100
#>       Module DummyPrefixFemale DummyPrefixMale Complexity Herm UseAge CalcLLR
#> Specs    ped                 F               M       full   no    yes    TRUE
#>       ErrFlavour SequoiaVersion           TimeStart             TimeEnd
#> Specs version2.0         2.3.18 2022-12-17 13:26:47 2022-12-17 13:29:23
SummarySeq(SeqOUT_HSg5)