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DNA_Crohn.Rmd
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DNA_Crohn.Rmd
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---
title: "Analysis of Methylation for Crohn's Disease"
author: "Ming-Chen Lu, mingchlu@umich.edu"
date: "`r format.Date(Sys.Date(), '%B %d, %Y')`"
geometry: "left = 2cm, right = 2cm, top = 2cm, bottom = 2cm"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(root.dir = './Desktop/DNA_Crohn',
results = 'asis', message = FALSE,
fig.height = 4)
library(tidyverse)
library(data.table)
library(future)
source('DNA_Crohn.R')
```
### Comparing adipocyte methylation in Crohn's to Non-Crohn's
The plot shows that the probe group of ch.14 seems to be over-represented.
```{r q2_hist, echo = FALSE}
plot
```
### Timing Comparison
```{r q2_time, echo = FALSE}
cat(sprintf("Time for computing the 1,000 permutations. \n
part h - sequential: %5.3fs \n
part i - mclapply: %5.3fs \n
part j - futures: %5.3f", t1[3], t2[3], t3[3]))
```
\pagebreak
### Results
```{r q2_table, echo = FALSE}
cap = paste("*P-values for testing whether the observed T score for each group",
"is larger than expected under the null hypothesis that patterns",
"of gene expression are the same across the Crohn's and",
"non-Crohn's groups after 1000 permutations.*")
knitr::kable(tbl, caption = cap)
```