Version2_Feasibility.Rmd

---
title: "R Notebook"
output: html_notebook
---

```{r load_libs}
library(tidyverse)
library(limma)
```


```{r make_data}
data.conditions <- LETTERS[1:4]
data.replicates <- 6
data.rows       <- 1e3
data.cols       <- length(data.conditions) * data.replicates
pheno.table     <- data.frame(SampleType = rep(data.conditions, each = data.replicates)) %>% 
                   mutate(Batch  = c(rep(1,3),rep(2,6),rep(3,6),rep(4,6),rep(5,3)),
                          Batch  = as.factor(Batch),
                          Sample = paste0(1:nrow(.), SampleType))
data.mat        <- rnorm(data.rows*data.cols, 7, 2) %>% 
                   matrix(ncol = data.cols) %>% 
                   `colnames<-`(pheno.table$Sample) %>% 
                   `rownames<-`(paste0("PROBE_",1:data.rows))
```


```{r fit_model}
design           <- model.matrix(~0 + SampleType + Batch, data = pheno.table)
colnames(design) <- colnames(design) %>% gsub("SampleType","",.)
contrasts        <- combn(length(data.conditions),2) %>% t
for(i in 1:nrow(contrasts)) {
  contrasts[i,1] <- data.conditions[as.numeric(contrasts[i,1])]
  contrasts[i,2] <- data.conditions[as.numeric(contrasts[i,2])]
}
contrasts        <- paste0(contrasts[,1], "-", contrasts[,2]) %>% 
                    `names<-`(gsub(" - ","_Vs_",.)) %>% 
                    makeContrasts(contrasts = ., levels = colnames(design))

fit              <- lmFit(data.mat, design) %>% 
                    contrasts.fit(contrasts = contrasts) %>% 
                    eBayes
```


```{r run_test}
tt <- topTable(fit, coef = "A-D")
```