---
title: "16-Apul methylkit"
author: Steven Roberts
date: "`r format(Sys.time(), '%d %B, %Y')`"  
output: 
  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(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
)
```


https://github.com/urol-e5/timeseries_molecular/blob/main/M-multi-species/data/e5_DNA_Azenta_metadata.csv

```{r}
analysisFilescov <- list(
  "../output/15-Apul-bismark/1H6_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1D7_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1D8_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1A9_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1D10_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/2B3_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/2G1_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1E3_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1F11_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1A8_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1D3_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1D9_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1D4_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1A2_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1B9_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1C4_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1A10_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1B10_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1C10_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov",
  "../output/15-Apul-bismark/1H8F1_R1_001.fastp-trim_bismark_bt2.CpG_report.merged_CpG_evidence.cov"
)
```

```{r}
myobj = methRead(location = analysisFilescov, sample.id = list("225", "229", "237", "244", "265", "139", "145", "150", "173", "186", "225", "229", "237", "244", "265", "139", "145", "150", "173", "186"), assembly = "Apul", pipeline = "bismarkCoverage", context="CpG", mincov=2, treatment = c(0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1))
```