*Please download the file homework11.R and write your
results there. Send the your answers to my
mailbox.*

# 1. GC content

Now that we have more powerful tools, we will explore again the GC
content of *Carsonella rudii*. First, we will see that GC content
can be seen as the average of an event.

## 1.1 Is this nucleotide G or C?

Please write a function called `is_G_or_C`

that determines
if a nucleotide is either *“G”* or *“C”*. The function
takes a *character vector* (called `dna`

) and returns
a *logic vector* called `ans`

. If `dna[i]`

is *“G”, “g”, “C”* or *“c”*, then `ans[i]`

is
`TRUE`

, otherwise it is `FALSE`

.

```
<- function(dna) {
is_G_or_C # write here
}
```

Test your function with the following code:

`is_G_or_C(c("a","c","t","g"))`

`[1] FALSE TRUE FALSE TRUE`

`is_G_or_C(c("A","C","T","G"))`

`[1] FALSE TRUE FALSE TRUE`

`mean(is_G_or_C(c("A","C","T","G")))`

`[1] 0.5`

As you can see, the GC content can be seen as the *mean* of
the event `is_G_or_C()`

. It is natural to think that we can
also calculate the variance and the standard deviation. How can we do
that?

## 1.2 Simulating some genes

We will use this function over simulated data. We need 100 genes of
different lengths. Please create a *vector*, called
`sim_gene_length`

, with 100 elements taken randomly (with
replacement) from the values 100, 103, 106, …, 1201. Then create a
*list*, called `sim_genes`

, with “random DNA
sequences”^{1}. Each element
`sim_genes[[i]]`

must be a random character vector with
length `sim_gene_length[i]`

. Only the letters “A”,“C”,“G”,
and “T” are valid, and all have the same probability.

After you have created `sim_genes`

, calculate the
*mean* of `is_G_or_C()`

for each gene and store them
in the vector `sim_mean_GC`

. You also need to calculate the
*variance* of `is_G_or_C()`

for each gene and store
the result in `sim_var_GC`

.

Finally, calculate the *standard error of the mean* by taking
the square root of `sim_var_GC`

divided by
`sim_gene_length`

, and store it in
`sim_std_err_mean`

.

`# write here`

Test your results with this code:

```
par(mfrow=c(2,2))
hist(sim_mean_GC, col="grey")
hist(sim_var_GC, col="grey")
hist(sim_gene_length, col="grey")
hist(sim_std_err_mean, col="grey")
```

## 1.3 Genes versus genome

Since all genes are taking from a random population, and all
nucleotides have the same probability, then **in this
case** we know that the *genome GC content*^{2} is
0.5.

But in many cases we do not have the full genome, just some genes.
**We want use the information of each gene to build a confidence
interval for the genome GC content.**

Fortunately we know that, if the genes are random DNA sequences, the
GC content of the genes is not too different from the GC content of the
genome^{3}. Moreover, we know that the GC
content of the genes is a random variable following the Normal
distribution^{4}.

Unfortunately, we do not know the standard deviation of the
population (we are using each gene as a sample). Instead, we can
approximate it with the standard error of each gene^{5},
but we will have to use the *Student’s t* distribution.

We start by choosing the confidence level \(1-\alpha=95\%\), therefore
`alpha`

is 0.05. You must use the function `qt()`

to find *the number of standard errors* `k`

that will
give you the confidence interval. Remember that the number of
*degrees of freedom* is `sim_gene_length-1`

.

Then you must calculate the vectors `sim_lower`

, with the
lower limits of each confidence interval, and `sim_upper`

,
with the upper limits.

```
<- 0.05
alpha # write here
```

Now you can count how many of the confidence intervals really contained the real value. In other words, you can see how good was the prediction.

`mean(sim_lower <= 0.5 & 0.5 <= sim_upper)`

`[1] 0.96`

You can see your results with this code:

```
<- 1:length(sim_genes)
gene_order plot(gene_order, sim_mean_GC, pch=16, ylim=c(0.3, 0.7))
arrows(gene_order, sim_upper, gene_order, sim_lower,
angle=90, code=3, length = 0.02)
abline(h=0.5, col="red")
```

The previous plot is hard to see, because there is a lot of
variability. It can be a little easier if we use the function
`order()`

to sort the values, as in the following code:

```
<- order(sim_mean_GC)
sorted plot(gene_order, sim_mean_GC[sorted], pch=16, ylim=c(0.3, 0.7))
arrows(gene_order, sim_upper[sorted], gene_order, sim_lower[sorted],
angle=90, code=3, length = 0.02)
abline(h=0.5, col="red")
```

# 2. Apply to real data

Now we will use this function over the genes of *Carsonella
rudii*.

## 2.1 Read the genes from a file

Please download the file `c_rudii.fna.txt`

and save it in your computer. It has to be stored in your computer to be
fast and efficient.

Using the library `seqinr`

, please write the code to

- read the FASTA file and load all genes in a list called
`genes`

, - calculate the mean of
`is_G_or_C()`

for each gene, and store each value in a vector called`mean_is_G_or_C`

. The length of this vector must be the number of genes - calculate the variance of
`is_G_or_C()`

for each gene, and store each value in a vector called`var_is_G_or_C`

. - calculate the length of each gene, and store each value in a vector
called
`gene_length`

. - calculate the
*standard error of the mean*for each gene. That is, the square root of the variance divided by the gene length.

`# write here`

Test your results with this code:

`length(genes)`

`[1] 182`

```
par(mfrow=c(2,2))
hist(mean_is_G_or_C, col="grey")
hist(var_is_G_or_C, col="grey")
hist(gene_length, col="grey")
hist(std_err_mean, col="grey")
```

## 2.2 Using genes to estimate genome GC content

We want use the information of the real genes to build a confidence
interval for the *genome GC content*.

Since the values have much more variability than in the simulation,
we choose a confidence level of \(1-\alpha=99.9\%\), therefore
`alpha`

is 0.001. You must use the function `qt()`

to find *the number of standard errors* `k`

that will
give you the confidence interval. Remember that the number of
*degrees of freedom* is `gene_length-1`

.

Then you must calculate the vectors `lower`

, with the
lower limits of each confidence interval, and `upper`

, with
the upper limits.

```
<- 0.001
alpha # write here
```

Test your results with this code:

```
<- 1:length(genes)
gene_order plot(gene_order, mean_is_G_or_C, pch=16, ylim=c(0, 0.4))
arrows(gene_order, upper, gene_order, lower,
angle=90, code=3, length = 0.02)
```

The previous plot is hard to see, because there is a lot of
variability. It can be a little easier if we use the function
`order()`

to sort the values, as in the following code:

```
<- order(mean_is_G_or_C)
sorted plot(gene_order, mean_is_G_or_C[sorted], pch=16, ylim=c(0, 0.4))
arrows(gene_order, upper[sorted], gene_order, lower[sorted],
angle=90, code=3, length = 0.02)
```