Get consensus genotype
getConsensusGeno(geno, maxNAfrac = 0.499, lowconf.NAfrac = 0.751)A vector with scores (0..ploidy or NA) for all samples of one parent.
The maximum fraction of missing scores allowed to assign a high-confidence consensus geno score; if more are missing a missing geno score is returned (the default requires MORE than half of the samples to be scored, so one missing out of 2 samples already causes a missing geno)
if the fraction missing scores is more than maxNAfrac but less than lowconf.NAfrac,
or if there is only one sample, a lowconf.geno score is assigned
Returns a list with 4 components:
The consensus of the dosages in vector geno. NA if geno is empty,
if all elements of geno are NA, if there are different non-NA
values in geno, or if the fraction of NA values in geno larger than maxNAfrac
If there is no conflict and the fraction of missing scores
is between maxNAfrac and lowconf.NAfrac, the consensus is assigned
as a "low-confidence" geno - this needs confirmation from the
F1 segregation to be accepted
TRUE if there are different non-NA values in geno, else FALSE
The fraction NA in geno (0.5 if length(geno)==0)