R Notebook

library(genotype)

n.sim = 10000
homogenotypes = rep('A')

Impacte de la profondeur de séquençage

p.hetero = 1/1000
error.rate = 1/100
merror = error_jc(rate = error.rate)
couvertures =1:50

success.homo = numeric(length = length(couvertures))
i = 0
for (c in couvertures) {
  s = simulate_sites(rep('A',n.sim),
                     rep('A',n.sim),
                     coverage = c,
                     error = merror)
  g = genotyping(s,sequencing.error = error.rate,phetero = p.hetero)
  i = i+1
  success.homo[i] = sum(g$ok) 
}

plot(couvertures,success.homo,type = "b",cex=0.5,log="x")

s = simulate_sites(rep('A',n.sim),
                     rep('A',n.sim),
                     coverage = 10,
                     error = merror)
g = genotyping(s,sequencing.error = error.rate,phetero = p.hetero)
hist(log10(g$score))

s = simulate_sites(rep('A',n.sim),
                     rep('A',n.sim),
                     coverage = 30,
                     error = merror)
g = genotyping(s,sequencing.error = error.rate,phetero = p.hetero)
hist(log10(g$score))

success.hetero = numeric(length = length(couvertures))
i = 0
for (c in couvertures) {
  s = simulate_sites(rep('A',n.sim),
                     rep('T',n.sim),
                     coverage = c,
                     error = merror)
  g = genotyping(s,sequencing.error = error.rate,phetero = p.hetero)
  i = i+1
  success.hetero[i] = sum(g$ok) 
}

plot(couvertures,success.hetero,type = "b",cex=0.5,col="blue",log="x")
points(couvertures,success.homo,type = "b",cex=0.5,col="red")

s = simulate_sites(rep('A',n.sim),
                     rep('T',n.sim),
                     coverage = 10,
                     error = merror)
g = genotyping(s,sequencing.error = error.rate,phetero = p.hetero)
hist(log10(g$score))

s = simulate_sites(rep('A',n.sim),
                     rep('T',n.sim),
                     coverage = 30,
                     error = merror)
g = genotyping(s,sequencing.error = error.rate,phetero = p.hetero)
hist(log10(g$score))

Impact du taux d’erreur

p.hetero = 1/1000
error.rate = 10^seq(from = -4,to = -1, length.out = 50)
couverture = 10

success.homo = numeric(length = length(error.rate))
i = 0
for (e in error.rate) {
  merror = error_jc(rate = e)
  s = simulate_sites(rep('A',n.sim),
                     rep('A',n.sim),
                     coverage = couverture,
                     error = merror)
  g = genotyping(s,sequencing.error = e,phetero = p.hetero)
  i = i+1
  success.homo[i] = sum(g$ok) 
}

plot(error.rate,success.homo,type = "b",cex=0.5,log="x")

success.hetero = numeric(length = length(error.rate))
i = 0
for (e in error.rate) {
  merror = error_jc(rate = e)
  s = simulate_sites(rep('A',n.sim),
                     rep('T',n.sim),
                     coverage = couverture,
                     error = merror)
  g = genotyping(s,sequencing.error = e,phetero = p.hetero)
  i = i+1
  success.hetero[i] = sum(g$ok) 
}

plot(error.rate,success.hetero,type = "b",cex=0.5,col="blue",log="xy",ylim=c(2000,10000))
points(error.rate,success.homo,type = "b",cex=0.5,col="red")