---
title: "Methylkit"
author: Steven Roberts
date: "`r format(Sys.time(), '%d %B, %Y')`" 
output: 
  github_document:
    toc: true
    toc_depth: 3
    number_sections: true
    html_preview: true
  html_document:
    theme: readable
    highlight: zenburn
    toc: true
    toc_float: true
    number_sections: true
    code_folding: show
    code_download: true
---

```{r setup, include=FALSE, }
library(knitr)
library(tidyverse)
library(kableExtra)
library(DESeq2)
library(pheatmap)
library(RColorBrewer)
library(data.table)
library(DT)
library(Biostrings)
library(methylKit)
knitr::opts_chunk$set(
  echo = TRUE,         # Display code chunks
  eval = FALSE,         # Evaluate code chunks
  warning = FALSE,     # Hide warnings
  message = FALSE,     # Hide messages
  fig.width = 6,       # Set plot width in inches
  fig.height = 4,      # Set plot height in inches
  fig.align = "center" # Align plots to the center
)
```

```{r, engine='bash'}
rsync -avz gannet.fish.washington.edu:/volume2/web/seashell/bu-github/2018_L18-adult-methylation/analyses/myobj_all /home/shared/8TB_HDD_02/sr320/scratch/ceabigr/
```


```{r, eval=TRUE, cache=TRUE}
load("/home/shared/8TB_HDD_02/sr320/scratch/ceabigr/myobj_all")
```


```{r, eval=TRUE, cache=TRUE}
filtered.myobj=filterByCoverage(myobj_all,lo.count=10,lo.perc=NULL,
                                      hi.count=NULL,hi.perc=98)

meth_filter=unite(filtered.myobj, min.per.group=NULL, destrand=TRUE)
```

```{r, eval=TRUE}
clusterSamples(meth_filter, dist="correlation", method="ward", plot=TRUE)


PCASamples(meth_filter)

```


cluster

![](http://gannet.fish.washington.edu/seashell/snaps/Monosnap_RStudio_Server_2023-07-24_16-34-06.png)