When running the following duplicate check & parentage assignment within the sequoia package:
ParOUT <- sequoia(GenoM = Geno, LifeHistData = LH, Err=0.005, Module="ped",
UseAge = "no",
quiet = FALSE, Plot = TRUE)
I get the following output and error (last two lines):
Warning: There are 2111 SNPs scored for <5% of individuals, these will be excluded
Warning: There are 1 monomorphic (fixed) SNPs, these will be excluded
Warning: In addition, there are 52874 SNPs scored for <50% of individuals
Warning: *********** There are 8 individuals scored for <5% of SNPs, these WILL BE IGNORED ***********
After exclusion, There are 40 individuals and 185843 SNPs.
Ageprior: Flat 0/1, overlapping generations, MaxAgeParent = 4,4
Error in if (!is.double(MAF) || any(MAF < 0 | MAF > 1)) { :
missing value where TRUE/FALSE needed
What is if (!is.double(MAF) || any(MAF < 0 | MAF > 1)) {} checking for that might be missing from my data?
I tried the above as well as running Module= as both "ped" and "par" with no difference in results.
