eda_chrom-states.Rmd

---
title: "eda_chrom-states.Rmd"
author: "Jason Torres"
date: "April 25, 2017"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Setup 

```{r}
# Approach originally proposed by Parker et al. 2013. PNAS 

"%&%" <- function(a,b) paste0(a,b)
library("dplyr")
library("data.table")

pre <- "/Users/jtorres/FUSE/" 
in.dir <- pre %&% "reference/islet/"
cur.dir <- in.dir %&% "stretch_enhancers/"

cs.df <- fread(in.dir %&% "Pancreat_islet_15_dense.reformatted_colours.bed",sep="\t")
cs.df$len <- cs.df$V3 - cs.df$V4

```


Write subsetted file with only weak,strong enhancer states (6,7,8,9)

```{r}

sub.df <- filter(cs.df,V4==6 | V4==7 | V4==8 | V4==9) %>% select(one_of("V1","V2","V3","V4"))
write.table(sub.df,file=cur.dir%&%"Pancreat_islet_15_dense.en-only.bed",col.names=F,row.names=F,
            sep="\t",quote=F)
```

Create merged enhancer file 

```{bash}
sh merge.sh
```


Get distribution 

```{r}

en.df <- fread(cur.dir %&% "islet_merged_enhancers.bed")
en.df$len <- en.df$V3 - en.df$V2
hist(en.df$len,breaks=100)

summary(en.df$len/1000)
qua <- quantile(en.df$len/1000,probs=seq(0,1,0.05))
q90 <- qua[grepl(pattern="90%",names(qua))] # 4.2 kb 

st.df <- filter(en.df,len>=q90*1000)
write.table(st.df,file=cur.dir%&%"Pancreat_islet_15_dense.en-only.perc90.bed",col.names=F,row.names=F,
            sep="\t",quote=F)

```


Make stretch enhancer bed 

```{bash}
sh merge2.sh 
```

Evalute stretch enhancer bed 

```{r}
s.df <- fread(cur.dir %&% "Pancreat_stretch-enhancers.bed")
s.df$len <- s.df$V3 - s.df$V2
```