Creating a new variable column based on data from another column - r

Question

I'm pretty new to R, and programming in general, and I'm wondering the best way to loop through a column so I can add a column to the data frame further describing the observations I looped through.
I currently have a list of amino acids and their positions on a protein that looks like this:
Residue Position
H 1
R 2
K 3
D 4
E 5
H 6
R 7
K 8
D 9
E 10
I'd like something that looks like this (where H, R, and K are basic amino acids, and D and E are acidic amino acids):
Residue Position Properties
H 1 Basic
R 2 Basic
K 3 Basic
D 4 Acidic
E 5 Acidic
H 6 Basic
R 7 Basic
K 8 Basic
D 9 Acidic
E 10 Acidic
I'm really not sure where to start, and I'm having difficulty finding a good resource for this kind of situation in R.
I started by trying to subset the data, but then I realized that wouldn't do the trick:
Basic
h.dat <- subset(all, all$Residue == "H")
r.dat <- subset(all, all$Residue == "R")
k.dat <- subset(all, all$Residue == "K")
Acidic
d.dat <- subset(all, all$Residue == "D")
e.dat <- subset(all, all$Residue == "E")
Thanks!
Note:
H = Histidine (Basic amino acid)
R = Arginine (Basic)
K = Lysine (Basic)
E = Glutamic Acid (Acidic)
D = Aspartic Acid (Acidic)

Answer 1

You can use ifelse. If df is the name of your original data,
df$Property <- ifelse(df$Residue %in% c("H", "R", "K"), "Basic", "Acidic")
df
# Residue Position Property
# 1 H 1 Basic
# 2 R 2 Basic
# 3 K 3 Basic
# 4 D 4 Acidic
# 5 E 5 Acidic
# 6 H 6 Basic
# 7 R 7 Basic
# 8 K 8 Basic
# 9 D 9 Acidic
# 10 E 10 Acidic

Answer 2

Try:
> df1
Residue Position
1 H 1
2 R 2
3 K 3
4 D 4
5 E 5
6 H 6
7 R 7
8 K 8
9 D 9
10 E 10
Create a reference table:
> df2
Residue Property
1 H Basic
2 R Basic
3 K Basic
4 D Acidic
5 E Acidic
Then merge:
> merge(df1, df2)
Residue Position Property
1 D 9 Acidic
2 D 4 Acidic
3 E 5 Acidic
4 E 10 Acidic
5 H 1 Basic
6 H 6 Basic
7 K 8 Basic
8 K 3 Basic
9 R 7 Basic
10 R 2 Basic

Answer 3

I think you might want to allow for non-polar amino acids as well:
c(rep("Basic",3),rep("Acidic",2),"Non-Polar")[ # those are the choices
match(dat$Residue, c("H","R","K","E","D"), nomatch=6) ] #select indices
So I added an 11th residue named "Z" and tested:
> dat$Property <- c(rep("Basic",3),rep("Acidic",2),"Non-Polar")[
match(dat$Residue, c("H","R","K","E","D"), nomatch=6) ]
> dat
Residue Position Property
1 H 1 Basic
2 R 2 Basic
3 K 3 Basic
4 D 4 Acidic
5 E 5 Acidic
6 H 6 Basic
7 R 7 Basic
8 K 8 Basic
9 D 9 Acidic
10 E 10 Acidic
11 Z 11 Non-Polar