---
output: html_document
---
```{r}
library(qtl)
library(ggplot2)

#read phenotypes and map
cross <- read.cross("csv","~/Dropbox/projects/vollenhovia/linkage","linkage map.csv",estimate.map=FALSE)
error_rate <- 0.00256  #estimated from GQ data
cross <- jittermap(cross)

plotMap(cross, show.marker.names=FALSE)

sex_scan <- scanone(cross,pheno.col=2, model="binary",method="em")
sex_scan_perm <- scanone(cross,pheno.col=2, model="binary",method="em",n.perm=1000)
summary(sex_scan, perms=sex_scan_perm, alpha=0.05, pvalues=TRUE)
plot(sex_scan)
cp <- as.numeric(summary(sex_scan, perms=sex_scan_perm, alpha=0.05, pvalues=TRUE)$chr)
qp <- summary(sex_scan, perms=sex_scan_perm, alpha=0.05, pvalues=TRUE)$pos

cross <- sim.geno(cross)
qtl <- makeqtl(cross, cp, qp)

lod.sex <- fitqtl(cross, pheno.col=2, qtl, formula=y~Q1*Q2, method="hk")
summary(lod.sex)
ggplot(sex_scan,aes(x=pos, y=lod, group=chr))+geom_line()+facet_grid(~chr,scale="free_x")+my_theme()+geom_hline(aes(yintercept=summary(sex_scan_perm)[[1]],color="red"))+xlab("linkage group")+ylab("LOD")+theme( axis.text.x = element_blank(),text=element_text(family="Helvetica"))

for(i in cp) print(bayesint(sex_scan,chr=i,prob=0.99))
```