sQTLs.Rmd

---
title: "R Notebook"
output: html_notebook
---

```{r}
library(data.table)
library(ggplot2)
library(cowplot)
library(Hmisc)
```


```{r}

sQTLs_upstream <- fread("./sQTL/upstream_eqtl_results.txt")
sQTLs_downstream <- fread("./sQTL/downstream_eqtl_results.txt")
```



#####


```{r}

sQTL_up <- sQTLs_upstream[source=="All_sqtls.bed.hg19" , ]
sQTL_down <- sQTLs_downstream[source=="All_sqtls.bed.hg19" , ]

SNP_up <- sQTLs_upstream[source=="All_SNPs.bed.hg19" , ]
SNP_down <- sQTLs_downstream[source=="All_SNPs.bed.hg19", ]

sQTL_up[, pos:="upstream"]
sQTL_down[, pos:="downstream"]

SNP_up[, pos:="upstream"]
SNP_down[, pos:="downstream"]


sQTL_SNP_up <- merge(sQTL_up, SNP_up, by="bin")
sQTL_SNP_down <- merge(sQTL_down, SNP_down, by="bin")

sQTL_SNP_up[, adj_enchiment:=(enrichment.x/enrichment.y)]
sQTL_SNP_down[, adj_enchiment:=(enrichment.x/enrichment.y)]
```


```{r}
sQTL_SNP_down[, `eQTLs in bin overlapping G4s.x`/`eQTLs in bin.x`]
```


```{r}
#sQTL_SNP_up_bin <- sQTL_SNP_up[, binconf(`enrichment.x`,   `enrichment.y`)]
#sQTL_SNP_down_bin <- sQTL_SNP_down[, binconf(`eQTLs in bin overlapping G4s.x`/`eQTLs in bin.x`,   `G4 bps in window.x`/`bps in bin.x`)]


#sQTL_SNP_up <- cbind(sQTL_SNP_up, sQTL_SNP_up_bin)
#sQTL_SNP_down <- cbind(sQTL_SNP_down, sQTL_SNP_down_bin)
```






```{r}
head(sQTLs_upstream[source=="All_sqtls.bed.hg19", ])
```

```{r}

```



```{r}
norm_sQTL_up <- ggplot(sQTL_SNP_up, aes(bin, adj_enchiment)) +
  geom_point( ) +
  geom_smooth(method="loess") +
  xlim(c(-500,50)) +
  ylim(c(0.75,2)) +
  xlab("Window position (25-nt)") +
  ylab("Adjusted sQTL enrichment over G4s")+
  geom_hline(yintercept=1, linetype="dashed", color = "red") +
  theme_bw() 


norm_sQTL_down <- ggplot(sQTL_SNP_down, aes(bin, adj_enchiment) ) +
  geom_point( ) +
  geom_smooth() +
  xlim(c(-50,500)) +
  ylim(c(0.75,2)) +
  xlab("Window position (25-nt)") +
  ylab("Adjusted sQTL enrichment over G4s")+
  geom_hline(yintercept=1, linetype="dashed", color = "red") +
  theme_bw()

```



```{r, fig.height=4, fig.width=7}
plot_grid(norm_sQTL_up, norm_sQTL_down, nrow=1)
```