---
title: "HW5 - Programming in R"
linkTitle: "HW5: R Programming"
description: >
type: docs
weight: 305
---

<br></br>

<div style="text-align: right"> 
Source code downloads: &nbsp; <a href="https://raw.githubusercontent.com/tgirke/GEN242//main/content/en/assignments/Homework/HW05/HW05.R" target="_blank">[ .R ]</a>
</div>

## A. Reverse and complement of DNA

__Task 1__: Write a `RevComp` function that returns the reverse and complement of a DNA sequence string. Include an argument that will allow to return only (i) the reversed sequence, (ii) the complemented sequence, or (iii) the reversed and complemented sequence. The following R functions will be useful for the implementation: 


Generate a short test DNA sequence
```r
x <- c("ATGCATTGGACGTTAG")  
x
```

```
## [1] "ATGCATTGGACGTTAG"
```

Vectorize sequence
```r
x <- substring(x, 1:nchar(x), 1:nchar(x)) 
x
```

```
##  [1] "A" "T" "G" "C" "A" "T" "T" "G" "G" "A" "C" "G" "T" "T" "A" "G"
```

Reverse sequence
```r
x <- rev(x) 
x
```

```
##  [1] "G" "A" "T" "T" "G" "C" "A" "G" "G" "T" "T" "A" "C" "G" "T" "A"
```

Collapse sequence back to character string
```r
x <- paste(x, collapse="")
x
```

```
## [1] "GATTGCAGGTTACGTA"
```

Form complement of sequence
```r
chartr("ATGC", "TACG", x) 
```

```
## [1] "CTAACGTCCAATGCAT"
```

__Task 2__: Write a function that applies the `RevComp` function to many sequences stored in a vector. In addition, write an export function that saves the sequences 
generated under Tasks 1 and 2 to a file in FASTA format.  

## B. Translate DNA into Protein

__Task 3__: Write a function that will translate one or many DNA sequences in all three reading frames into proteins. The following commands will simplify this task:


Import lookup table of genetic code
```r
AAdf <- read.table(file="http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/AA.txt", header=TRUE, sep="\t") 
AAdf[1:4,]
```

```
##   Codon AA_1 AA_3 AA_Full AntiCodon
## 1   TCA    S  Ser  Serine       TGA
## 2   TCG    S  Ser  Serine       CGA
## 3   TCC    S  Ser  Serine       GGA
## 4   TCT    S  Ser  Serine       AGA
```

Generated named vector of relevant components
```r
AAv <- as.character(AAdf[,2]) 
names(AAv) <- AAdf[,1] 
AAv
```

```
## TCA TCG TCC TCT TTT TTC TTA TTG TAT TAC TAA TAG TGT TGC TGA TGG CTA CTG CTC CTT CCA CCG CCC CCT CAT 
## "S" "S" "S" "S" "F" "F" "L" "L" "Y" "Y" "*" "*" "C" "C" "*" "W" "L" "L" "L" "L" "P" "P" "P" "P" "H" 
## CAC CAA CAG CGA CGG CGC CGT ATT ATC ATA ATG ACA ACG ACC ACT AAT AAC AAA AAG AGT AGC AGA AGG GTA GTG 
## "H" "Q" "Q" "R" "R" "R" "R" "I" "I" "I" "M" "T" "T" "T" "T" "N" "N" "K" "K" "S" "S" "R" "R" "V" "V" 
## GTC GTT GCA GCG GCC GCT GAT GAC GAA GAG GGA GGG GGC GGT 
## "V" "V" "A" "A" "A" "A" "D" "D" "E" "E" "G" "G" "G" "G"
```

Tripletize sequence and translate by name subsetting/sorting of AAv
```r
y <- gsub("(...)", "\\1_", x) 
y <- unlist(strsplit(y, "_")) 
y <- y[grep("^...$", y)] 
AAv[y] 
```

```
## GAT TGC AGG TTA CGT 
## "D" "C" "R" "L" "R"
```

## Homework submission

Submit the 3 functions in one well structured and annotated R script to your
private GitHub repository under `Homework/HW5/HW5.R`. The script should include
instructions on how to use the functions.


## Due date

This homework is due on Fri, April 26th at 6:00 PM.

## Homework Solutions

See [here](https://raw.githubusercontent.com/tgirke/GEN242/main/static/custom/hw_solutions/hw5_solution.R).