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JiscaH / sequoia

R package for pedigree inference based on SNP data
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ErrM not found with DuplicateCheck #9

Closed sinnweja closed 3 years ago

sinnweja commented 3 years ago

From the example in the vignette, the call to sequoia with MaxSubIter=1, you get an error that it can't find ErrM in the DuplicateCheck function. However, ErrM is an element of ParOUT, so you should make sure to pass ParOUT$ErrM to DuplicateCheck. Here is code that gets the error and shows a work-around.

` library(sequoia") data(Ped_HSg5, LH_HSg5) set.seed(1000) Geno <- SimGeno(Ped = Ped_HSg5, nSnp = 200) Geno[1:5,1:5] ParOUT <- sequoia(GenoM = Geno, LifeHistData = LH_HSg5, MaxSibIter = 0) names(ParOUT) table(is.na(ParOUT$PedigreePar[,2])) SeqOUT <- sequoia(GenoM = Geno, SeqList = ParOUT, MaxSibIter = 1)

gets error

SeqOUT <- sequoia(GenoM = Geno, SeqList = ParOUT, MaxSibIter = 1, Err=1e-4)

gets error, but this allows ErrM to be found so it can run

ErrM <- ParOUT$ErrM SeqOUT <- sequoia(GenoM = Geno, SeqList = ParOUT, MaxSibIter = 1) `

JiscaH commented 3 years ago

Please see my reply to your other post.