bug in assocTestSingle if there are monomorphic SNPs

[uw-gac]

bug in assocTestSingle if there are monomorphic SNPs

[jonaszierer]

sorry the it actually should just be

freq$freq <- freq$freq[keep]
freq$MAC <- freq$MAC[keep]

[smgogarten]

freq is a data.frame, so the matrix-type subsetting should work. Can you show the error you're getting?

[jonaszierer]

.alleleFreq actually returns a list if sex is missing:

GENESIS/R/utils.R

Lines 65 to 75 in a822d2e

	# check sex
	sex <- validateSex(gdsobj)
	if (!is.null(sample.index)) sex <- sex[sample.index]
	if (is.null(sex)) {
	#freq <- 0.5*colMeans(geno, na.rm=TRUE)
	count <- colSums(geno, na.rm=TRUE)
	nsamp <- colSums(!is.na(geno))
	freq <- count/(2*nsamp)
	mac <- round(pmin(count, 2*nsamp - count))
	return(list(freq=freq, MAC=mac))
	}

[smgogarten]

Thanks! Fixed in 2bb43fd