Helper for Finding Target Variants for Screening

Use recombination distance (and preliminary single marker test results) to select target variants for screening

Usage

FindTargetVars(
  map,
  min.cM = 0.1,
  from = 1L,
  to = length(map),
  initial.targets = NULL,
  smt.thresh = NULL
)

map: a vector specifying the recombination map 'CDF' at all cached variants
min.cM: the desired minimum recombination distance between target loci in cM
from: the first variant index to consider as a target
to: the last variant index to consider as a target
initial.targets: an integer vector or data.frame. If an integer vector, the indices of variants that should be included in the returned targets. If a data.frame, single marker test results in the format returned by TestCachedMarkers to be used in combination with smt.thresh to implicitly define initial target variants
smt.thresh: when initial.targets is provided as a data.frame of single marker test results, a -log10 p-value threshold such that variants with any signal above that threshold should be included in initial targets

integer vector of target variant indices

if (FALSE) { # \dontrun{
} # }