Commit 38a353b5 authored by mariefbourdon's avatar mariefbourdon
Browse files

22074 paper

parent ab311e94
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......@@ -332,7 +332,6 @@ ggsave("figures/figS5.pdf",grid_scans,width=14,height = 5)
## Comparision of non mendelian/wrong alleles markers between the 4 datasets
A REFAIRE!!!!
```{r}
colnames(tab2_data2) <- c(colnames(tab2_data2)[1:3],paste0(colnames(tab2_data2)[4:ncol(tab2_data2)],".2"))
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......@@ -239,9 +239,62 @@ rec_ratios %>% mutate(group_rat=case_when(rat_prev<5 ~ 0,
rat_prev >=5 ~ 1)) %>%
group_by(group_rat) %>% summarise(n=n(),p=n()/nrow(rec_ratios))
#meansd of peak <5
rec_ratios %>% filter(rat_prev<5) %>% summarise(mean=mean(rat_prev),
sd=sd(rat_prev))
#max ratio
rec_ratios %>% summarise(max=max(rat_prev))
rm(mark,chr,pos,place,previous,follow,kn_previous,kn_follow,fol,kn_fol,kn_pos,kn_prev,i,prev)
```
## Other peaks
chr2 : max lod 6.72 on pseudomarkernext to marker with non mendelian proportions
```{r}
qtl_plot(pheno_before,lod=data.frame(group = c("alpha=0.05", "alpha=0.1","alpha=0.63"),
lod = threshold_before[1:3]),
ylab="LOD score",
chrs = "2",
size=0.6,
rug = TRUE) +
theme(legend.position = "none",
strip.background = element_blank(),
strip.text.x = element_blank()) +
theme(plot.title = element_text(face="plain",size=14))
```
chr7 : max lod 9.79 on pseudomarker next to marker with non mendelian proportions
```{r}
qtl_plot(pheno_before,lod=data.frame(group = c("alpha=0.05", "alpha=0.1","alpha=0.63"),
lod = threshold_before[1:3]),
ylab="LOD score",
chrs = "7",
size=0.6,
rug = TRUE) +
theme(legend.position = "none",
strip.background = element_blank(),
strip.text.x = element_blank()) +
theme(plot.title = element_text(face="plain",size=14))
```
chr8 : max lod 10.03 on marker with non mendelian proportions
```{r}
qtl_plot(pheno_before,lod=data.frame(group = c("alpha=0.05", "alpha=0.1","alpha=0.63"),
lod = threshold_before[1:3]),
ylab="LOD score",
chrs = "7",
size=0.6,
rug = TRUE) +
theme(legend.position = "none",
strip.background = element_blank(),
strip.text.x = element_blank()) +
theme(plot.title = element_text(face="plain",size=14))
```
## Use of stuart's functions
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......@@ -166,6 +166,36 @@ rec_ratios %>% mutate(group_rat=case_when(rat_prev<5 ~ 0,
rm(mark,chr,pos,place,previous,follow,kn_previous,kn_follow,fol,kn_fol,kn_pos,kn_prev,i,prev)
```
## other peaks
chr1 : max lod 8.054 on pseudomarker next to marker with non mendelian proportions
```{r}
qtl_plot(pheno_before,lod=data.frame(group = c("alpha=0.05", "alpha=0.1","alpha=0.63"),
lod = threshold_before[1:3]),
ylab="LOD score",
chrs = "1",
size=0.6,
rug = TRUE) +
theme(legend.position = "none",
strip.background = element_blank(),
strip.text.x = element_blank()) +
theme(plot.title = element_text(face="plain",size=14))
```
chr13 : max lod 8.236 on pseudomarker and its adjacent marker with non mendelian proportions
```{r}
qtl_plot(pheno_before,lod=data.frame(group = c("alpha=0.05", "alpha=0.1","alpha=0.63"),
lod = threshold_before[1:3]),
ylab="LOD score",
chrs = "13",
size=0.6,
rug = TRUE) +
theme(legend.position = "none",
strip.background = element_blank(),
strip.text.x = element_blank()) +
theme(plot.title = element_text(face="plain",size=14))
```
```{r}
#our genotypes
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% latex table generated in R 4.1.0 by xtable 1.8-4 package
% Tue Jun 28 15:09:14 2022
% Mon Jul 4 14:05:46 2022
\begin{table}[ht]
\centering
\begin{tabular}{llrr}
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