QC_analysis.Rmd

---
title: "chipQC_analysis"
output:
  word_document:
    toc: yes
    toc_depth: '4'
---

```{r setup, include=FALSE}
library(ChIPQC)
```

# QC
## Loading metadata

This analysis only examins chromosome 1. 

```{r metadata, message=TRUE,echo=FALSE}
samples = read.csv("sample_metafile.csv")
samples[,1:5]
```

## Loading files

```{r loading files, echo=FALSE,message=FALSE}
QC_data = ChIPQC(samples,annotaiton="mm10")
```

## Report: QC Summary table

```{r QC Summary table, echo=FALSE,message=TRUE}
QCmetrics(QC_data)
```