lme_all_plot.Rmd

# Exploratory plots of the linear mixed-effects model

```{r opts_chunk, echo=FALSE}
library(knitr)
opts_chunk$set(tidy=FALSE, fig.width=6, fig.height=6)
```

# Load the libraries
```{r library, message=FALSE}
library(lattice)
library(VennDiagram)
```

# Load the data
```{r load_data}
setwd('~/UBC Stats/STAT540/Group Project/')

# Load the M-values
load('Data/ALL_tall.Rdata')

# Load the results of the linear models
lm.t <- read.table('Data/lm.tab', stringsAsFactors=FALSE)
lme.t_reml <- read.table('Data/lme.tab', stringsAsFactors=FALSE)
lme.t_ml <- read.table('Data/lme_ml.tab', stringsAsFactors=FALSE)

# Load the sets gene hits
lm.geneset <- readLines('Data/lm-geneset.txt')
lme.geneset <- readLines('Data/lme-geneset.txt')
```

# Plot the M-values of a CpG island
```{r stripplot}
stripplot(M ~ Group | probe, tall,
	jitter = TRUE, auto.key = TRUE, type = c('p', 'a'),
	subset = cgi == lme.t_ml[1, 'cgi'],
	main='Strip plot of the probes of a single CpG island',
	ylab='M-value')
```

# Plot the denisty of the q-values of the linear model
```{r q_lm_q_density}
densityplot(lm.t$q,
	main='Density of q-values of the linear model',
	xlab='q-value')
```

# Plot the denisty of the t-statistic of the linear mixed-effects model
```{r lmer_t_density}
densityplot(lme.t_reml$t,
	main='Density of the t-statistic of the linear mixed-effects model',
	xlab='t-statistic')
```

# Venn diagram of the overlap of the hits of the fixed and mixed models
```{r venn_lm_lmer}
plot.new()
grid.draw(venn.diagram(list(
	LinearModel = lm.geneset,
	LinearMixedEffectsModel = lme.geneset),
	filename=NULL, fill=c('red', 'blue')))
```