Commit 2fea466f by Eric Coissac

Correction

parent 60c6ef81
---
title: "R Notebook"
output: html_notebook
---
```{r}
library(genotype)
```
```{r}
n.sim = 10000
homogenotypes = rep('A')
```
# Impacte de la profondeur de squenage
```{r}
p.hetero = 1/1000
error.rate = 1/100
merror = error_jc(rate = error.rate)
couvertures =1:50
```
```{r}
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$ok)
}
```
```{r}
plot(couvertures,success.homo,type = "b",cex=0.5,log="x")
```
```{r}
s = simulate_sites(rep('A',n.sim),
rep('A',n.sim),
coverage = 10,
error = merror)
g = genotyping(s,sequencing.error = error.rate,phetero = p.hetero)
hist(log10(g$score))
```
```{r}
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$score))
```
```{r}
success.hetero = numeric(length = length(couvertures))
i = 0
for (c in couvertures) {
s = simulate_sites(rep('A',n.sim),
rep('T',n.sim),
coverage = c,
error = merror)
g = genotyping(s,sequencing.error = error.rate,phetero = p.hetero)
i = i+1
success.hetero[i] = sum(g$ok)
}
```
```{r}
plot(couvertures,success.hetero,type = "b",cex=0.5,col="blue",log="x")
points(couvertures,success.homo,type = "b",cex=0.5,col="red")
```
```{r}
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$score))
```
```{r}
s = simulate_sites(rep('A',n.sim),
rep('T',n.sim),
coverage = 30,
error = merror)
g = genotyping(s,sequencing.error = error.rate,phetero = p.hetero)
hist(log10(g$score))
```
# Impact du taux d'erreur
```{r}
p.hetero = 1/1000
error.rate = 10^seq(from = -4,to = -1, length.out = 50)
couverture = 10
```
```{r}
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$ok)
}
```
```{r}
plot(error.rate,success.homo,type = "b",cex=0.5,log="x")
```
```{r}
success.hetero = numeric(length = length(error.rate))
i = 0
for (e in error.rate) {
merror = error_jc(rate = e)
s = simulate_sites(rep('A',n.sim),
rep('T',n.sim),
coverage = couverture,
error = merror)
g = genotyping(s,sequencing.error = e,phetero = p.hetero)
i = i+1
success.hetero[i] = sum(g$ok)
}
```
```{r}
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")
```
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