search for: misinherit

...is a locus whose data trips up the tdt function. And when it does, it short circuits the entire loop. Nothing gets written to Resultdt. > Resultdt<-lapply(PGWide[,240:389], tdt) Error in rep.default(1, nrow(U)) : rep() incorrect type for second argument In addition: Warning messages: 1: 1 misinheritances in: phase.resolve(g.cs, g.mr, g.fr, as.allele.pair = TRUE, allow.ambiguous = (parent == 2: 1 misinheritances in: phase.resolve(g.cs, g.mr, g.fr, as.allele.pair = TRUE, allow.ambiguous = (parent == 3: 4 misinheritances in: phase.resolve(g.cs, g.mr, g.fr, as.allele.pair = TRUE, allow.ambiguou...

...("messed up") else > > print("works") > [1] "works" > [1] "works" > [1] "works" > [1] "works" > Error in rep.default(1, nrow(U)) : rep() incorrect type for > second argument In addition: Warning messages: > 1: 1 misinheritances in: phase.resolve(g.cs, g.mr, g.fr, > as.allele.pair = TRUE, allow.ambiguous = (parent == > 2: 2 misinheritances in: phase.resolve(g.cs, g.mr, g.fr, > as.allele.pair = TRUE, allow.ambiguous = (parent == > 3: 2 misinheritances in: phase.resolve(g.cs, g.mr, g.fr, > as.allele.pa...

...info", value, entry) Apply this "fix" would result in snpMatrix's "R CMD check" churning out: --------------------- .ld.withmany: local variable ?names.components? assigned but may not be used .ld.withmany: local variable ?nsnps.for.each? assigned but may not be used misinherits: local variable ?nc.snps? assigned but may not be used misinherits: local variable ?nr.snps? assigned but may not be used qq.chisq: local variable ?lab? assigned but may not be used read.HapMap.data: local variable ?base? assigned but may not be used read.HapMap.data: local variable ?build? assign...