gene-expression-analysis.Rmd

---
title: "Gene Expression Analysis"
author: "Your Name"
date: '`r format(Sys.time(), "%d %b %Y")`'
output: html_document
---

Read the raw data files into R

```{r cache=TRUE}
genes <- read.delim("gene.description.txt")
subjects <- read.delim("cancer.patients.txt")
evals <- read.delim("gene.expression.txt",stringsAsFactors = FALSE)
```

The number of genes in the study is `r nrow(genes)` and there were `r nrow(subjects)` subjects

Here is a heatmap of the genes of interest

```{r echo=FALSE,warning=FALSE,message=FALSE}

##HIDE ME!!!
genelist <- c("ESR1", "NAT1", "SUSD3","SLC7A2" ,"SCUBE2")
probes <- na.omit(genes[match(genelist,genes[,2]),1])
exprows <- match(probes,rownames(evals))

library(RColorBrewer)
sampcol <- rep("blue", ncol(evals))
sampcol[subjects$er == 1 ] <- "yellow"
rbPal <- brewer.pal(10, "RdBu")
heatmap(as.matrix(evals[exprows,]),ColSideColors = sampcol,col=rbPal)
```

- Create a list of R packages and versions

```{r}

sessionInfo()
```