solution-exercise9.Rmd

---
title: "Exercise 9"
author: "Your Name"
date: '`r format(Sys.time(), "%d %b %Y")`'
output: pdf_document
---

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


```{r}
chr8Genes <- genes[genes$Chromosome=="chr8",]
head(chr8Genes)
```

```{r}
chr8GenesOrd <-chr8Genes[order(chr8Genes$Start),]
head(chr8GenesOrd)
```

```{r}
chr8Expression <- evals[match(chr8GenesOrd$probe,rownames(evals)),]
```

- Create a for loop to perform to test if the expression level of each gene on chromosome 8 is significantly different between ER positive and negative samples

```{r}
ngenes <- nrow(chr8Expression)
pvals <- NULL
for(i in 1:ngenes) {
  tmp <- t.test(as.numeric(chr8Expression[i,]) ~  subjects$er)
  pvals[i] <- tmp$p.value
  }
pvals
table(pvals < 0.05)
sum(pvals < 0.05)
```