Explanation for simulation stuff

N.thrs (NL.N.permutations in perm.R called by sum.threshold in study.R)
  n.lod x n.alpha
  quantiles of max.N across n.perm
  alpha-quantile across perms of max hotspot size for lod.thrs
max.N (NL.N.perm in perm.R)
  n.perm x n.lod
  maximum of count.thr across genome
  max hotspot size for lod.thrs across genome by perm
count.thr (count.thr in perm.R)
  chr.pos x n.lod
  count of traits with lod above lod.thrs at each genome position
  hotspot size for lod.thrs at genome position
per.scan (NL.N.perm in perm.R)
  chr.pos x n.phe
  genome scan using scanone (zero out values below smallest lod.thrs)
  lod score by genome position of traits

N.err
  n.lod x n.alpha
  outN / nSim
  proportion of data sets with max hotspot size for lod.thrs above alpha quantile across perms
outN.WW (sim.hotspot in study.R)
  n.lod x n.alpha
  count of data sets with max hotspot size for lod.thrs above alpha quantile across perms
N.counts (N.WW.counts called by sum.threshold in study.R)
  n.lod x n.alpha
  T/F: does data max hotspot size for lod.thrs exceed alpha quantile across perms
max (N.WW.counts in study.R)
  n.lod
  maximum of count.thr across genome
  max hotspot size for lod.thrs acros genome for simulated data
count.thr (count.thr in perm.R)
  chr.pos x n.lod
  count of traits with lod above lod.thrs at each genome position
  hotspot size for lod.thrs at genome position

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WW.thrs (WW.permutations in westwu.R called by sum.threshold in study.R)
  n.lod x n.alpha
  alpha quantile of max.hotspots.counts over permutations for each lod.thrs
max.WW (NL.N.perm in perm.R)
  n.perm x n.lod
  maximum of count.thr across genome
  max hotspot size for lod.thrs across genome by perm
count.thr (count.thr in perm.R)
  chr.pos x n.lod
  count of traits with lod above lod.thrs at each genome position
  hotspot size for lod.thrs at genome position
per.scan
  chr.pos x n.phe
  permute scan separately by trait across genome

WW.err
  n.lod x n.alpha
  outWW / nSim
  proportion of data sets with max westwu size for lod.thrs above alpha quantile across perms
outN.WW (sim.hotspot in study.R)
  n.lod x n.alpha
  count of data sets with max westwu size for lod.thrs above alpha quantile across perms
WW.counts (N.WW.counts called by sum.threshold in study.R)
  n.lod x n.alpha
  T/F: does data max westwu size for lod.thrs exceed alpha quantile across perms

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NL.counts (NL.counts called by sum.threshold in study.R)
  n.lod x n.alpha
NL.thrs (NL.N.permutations in perm.R called from sum.threshold in study.R)
  Nmax x n.alpha
  alpha quantiles across permutations for Nmax largest values.
max.lod.quant (NL.N.permutations in perm.R)
  n.perm x Nmax
  largest 1:Nmax upper quantiles across genome for each permutation
quant (NL.N.permutations in perm.R)
  chr.pos x Nmax
  1:Nmax upper quantiles across traits by genome position
per.scan (NL.N.permutations in perm.R)
  chr.pos x n.phe
  genome scan using scanone (zero out values below smallest lod.thrs)
  lod score by genome position of traits
  
count.thr (count.thr in perm.R)
  chr.pos x n.lod
  count of traits with lod above lod.thrs at each genome position
  hotspot size for lod.thrs at genome position
