PCAir unable to proceed when there are no related individuals

[uw-gac]

PCAir unable to proceed when there are no related individuals

[smgogarten]

pcair should return a list with $rels NULL in the case of no relatives. Could you provide some more context (what code did you run leading up to this error), and also sessionInfo()?

[seunghun23]

Below is the code, and I can not provide with sessionInfo() for now because one of my
colleague ran the script, and he did with a small vcf of his which includes only 11 samples (probably all unrelated with each other). The same script ran fine with larger vcfs before.

---

seqVCF2GDS(vcf_input,"temp.gds", verbose=FALSE)
gds<- seqOpen("temp.gds")

snpset <- snpgdsLDpruning(gds, method="corr", slide.max.bp=10e6,
ld.threshold=sqrt(0.1), verbose=FALSE)
pruned <- unlist(snpset, use.names=FALSE)
king <- snpgdsIBDKING(gds, snp.id=pruned, verbose=FALSE)
kingMat <- king$kinship
dimnames(kingMat) <- list(king$sample.id, king$sample.id)

pcs <- pcair(gds,
kinobj=kingMat, kin.thresh=2^(-9/2),
divobj=kingMat, div.thresh=-2^(-9/2),
snp.include=pruned)

[smgogarten]

pcairPartition (the function that selects an unrelated set) will run on a sample set that small (even with no relatives), so I suspect the problem might have arisen farther upstream in the script (as in, the inputs to the pcair function were not valid). But 11 samples is such a small number that I'm not sure it makes sense to run this analysis on them.