calc_qall: calc_qall...
In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

calc_qall ***********************************************************

1
2
3

calc_qall(Pvalue_threshold, fracInvalid_threshold, fracNA_threshold, Pvalue,
  fracInvalid, F1.NAfrac, matchParents, bestfit, bestParentfit, par.conflicts,
  par.NAfrac, critweight, parentsScoredWithF1)

`Pvalue_threshold`	Threshold can be disabled by setting to 0
`fracInvalid_threshold`	Threshold can be disabled by setting to 1
`fracNA_threshold`	Threshold can be disabled by setting to 1
`Pvalue`	P-value of bestParentfit segtype
`fracInvalid`	Fraction invalid scores of the bestParentfit segtype
`F1.NAfrac`	fraction missing scores among F1 samples
`matchParents`	Should parents match F1? One of the following: "No", "Unknown", "OneOK" or "Yes"
`bestfit`	segtype of best fit of population
`bestParentfit`	segtype of best fit of parents
`par.conflicts`	Logical vector: is there a conflict for P1, P2
`par.NAfrac`	number of NA scores for the samples of P1, P2
`critweight`	numeric vector of length 3 (3 quality criteria) with their weights, or NA (in that case qall = q1q2q3, not a weighted average)
`parentsScoredWithF1`	Were parents scored with F1?

vector of length 4 or 5. The last (two) components of the vector are qall_mult (obtained by multiplication of q1..q3), and if critweights is supplied, qall_weights (a weighted average of q1..q3)

mdavy86/polymapR documentation built on May 25, 2019, 9:35 p.m.