proxReg-Analysis.Rmd

---
title: "proxReg"
author: "Christopher T. Lee"
date: "11/13/2019"
output: html_document
---

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


# Running analysis

Download Supplementary Table 1 and place in working directory before proceeding.
```{r eval = F}
newpeaklist = gdata::read.xls("./Supplementary Table 1.xlsx", stringsAsFactors=F)
```

##### To download all the ENCODE ChIP-seq experiments used, follow this procedure:
```{r eval = F}
write.table(sprintf("%s.gz",newpeaklist$Dataset), "./ENCODE_datasets.txt", quote=F, row.names = F, col.names = F)
```

Run the following on bash in your working directory to download the ChIP-seq experiments:

Use `brew install wget` if wget is not already installed.
```
awk '{print "wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/"$1}' <(cut -f 1 ENCODE_datasets.txt | grep narrowPeak) > tfbs_wget.sh

bash tfbs_wget.sh
```

### Running proxReg on all data:
```{r eval = F}
library(chipenrich)
for (peak in newpeaklist$V1) {
	proxReg(peaks = peak, 
			out_name = sprintf("./%s.promoter",peak),
			out_path = getwd(),
			genome = "hg19",	
			reglocation = "tss",
			qc_plots = T,
			n_cores = 1
			)
}

for (peak in newpeaklist$V1) {
	proxReg(peaks = peak, 
			out_name = sprintf("./%s.enhancer",peak),
			out_path = getwd(),
			genome = "hg19",
			reglocation = "enhancer",
			qc_plots = T,
			n_cores = 1
			)
}
```