hdp_MutSigPipeline.Rmd

---
title: "hdp MutSig Pipeline"
output: html_notebook
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
setwd('/Users/quinlan/Documents/Quinlan-PhD/SpermSeq/') #wherever files are
list.files()
library(devtools)
setRepositories()
devtools::install_github("nicolaroberts/hdp", build_vignettes = FALSE)
library(hdp)

??hdp

mut_count <- read.csv('/Users/quinlan/Documents/Quinlan-PhD/SpermSeq/BloodMutationCountMatrix.csv')

devtools::install_github("WuyangFF95/SynSigRun", ref = "1.0.0-branch")
```
This is an [R Markdown](http://rmarkdown.rstudio.com) Notebook. When you execute code within the notebook, the results appear beneath the code. 

Try executing this chunk by clicking the *Run* button within the chunk or by placing your cursor inside it and pressing *Cmd+Shift+Enter*. 

```{r}
plot(cars)
```

Add a new chunk by clicking the *Insert Chunk* button on the toolbar or by pressing *Cmd+Option+I*.

When you save the notebook, an HTML file containing the code and output will be saved alongside it (click the *Preview* button or press *Cmd+Shift+K* to preview the HTML file). 

The preview shows you a rendered HTML copy of the contents of the editor. Consequently, unlike *Knit*, *Preview* does not run any R code chunks. Instead, the output of the chunk when it was last run in the editor is displayed.