Question

So I’m trying to do these problems in R in order to learn it.

But I’m stuck on the first problem to simply count the frequency of charactors in a string. I can’t even seem to get past loading the data and getting to the string 🙁

How do I do something like print the first charactor of the string from this text file?

Here’s what I’ve tried so far:

> rosalind_dna <- read.table("~/Downloads/rosalind_dna.txt", quote="")
Warning message:
In read.table("~/Downloads/rosalind_dna.txt", quote = "") :
  incomplete final line found by readTableHeader on '~/Downloads/rosalind_dna.txt'
>   viewData(rosalind_dna)
> str(rosalind_dna[1,1,1])
 Factor w/ 1 level "GGCCCGGTTACTGCGACTGAACAATCAAAATCTGAAGCATTTAAGCCAAACCAATTGAGATCGACTTACGAGCGATAACCCAGTATATTCAAGTGCTACTGATGAGGCGTGGTCCCCTGGACAAGGC"| __truncated__: 1

Answer 1

What you’ve done so far is just fine.

read.table returns a data frame. In this case, you just get a data frame with a single column and only a single value in that column.

By default, R will convert character columns in data frames to factors. You can convert it back using as.character.

Then you’ll simply want to split that single string into individual characters (strsplit) and then make a table (table). (No need for loops!)

Here’s a toy example illustrating all the functions I mentioned:

> dat <- data.frame(V1 = factor("abcdfjtusje"))
> str(dat)
'data.frame':   1 obs. of  1 variable:
 $ V1: Factor w/ 1 level "abcdfjtusje": 1
> x <- as.character(dat[1,1])
> x
[1] "abcdfjtusje"
> strsplit(x,"")
[[1]]
 [1] "a" "b" "c" "d" "f" "j" "t" "u" "s" "j" "e"

> strsplit(x,"")[[1]]
 [1] "a" "b" "c" "d" "f" "j" "t" "u" "s" "j" "e"
> table(strsplit(x,"")[[1]])

a b c d e f j s t u 
1 1 1 1 1 1 2 1 1 1 
>