将长字符串列表拆分为逗号分隔的向量，然后转换为 df 行

Question

I have gathered that this question is somewhat commonly asked, but I've hit a few snags that I can't seem to find an answer to.

I have a long string:

line1 = "GGCTTATTTAACGGGCAGATATACGCTGGGCAAATC..."

I want it to look like:

line1 = c("G", "G", "C", ...)

(As an aside, is it possible to have letters like above as integers - when I tried with the function as.integer, it converted it all to NAs?)

I have tried: strsplit(line1, "")

Which produces a list of: 'G''G''C'...

To solve this, I've tried: paste(line1, collapse = ", ")

Which sort of works: c(\"G\", \"G\", \"C"...)

When I tried to remove the ' \ ' with gsub , it didn't let be do it, as it suddenly registered everything in the script as in quotes.

Further, once this is done, I'd like to shape this into either a row or a column of a dataframe like so:

   [1] [2] [3] ...
[1] G   G   C

Or:

   [1]
[1] G
[2] G
[3] C

Answer 1

After splitting unlist the result, convert it to factor and then numeric:

fac <- factor(unlist(strsplit(line1, "")))
as.numeric(fac)
## [1] 5 5 4 6 6 3 6 6 6 3 3 4 5 5 5 4 3 5 3 6 3 6 3 4 5 4 6 5 5 5 4 3 3 3 6 4 1 2 2 2

# this gives the correspondence between numbers and characters
# i.e. space is 1, dot is 2, A is 3, C is 4, G is 5 and T is 6
levels(fac)
## [1] " " "." "A" "C" "G" "T"

The levels can also be specified explicitly using the levels= argument in which case other characters will be NA and optionally could be eliminated using na.omit(...).

fac <- factor(unlist(strsplit(line1, "")), levels = c("A", "C", "G", "T"))
as.numeric(fac)
## [1]  3  3  2  4  4  1  4  4  4  1  1  2  3  3  3  2  1  3  1  4  1  4  1  2  3  2  4  3  3  3  2  1  1  1  4  2 NA NA NA NA

Note

The input in the question is the following. Possibly the last 4 characters were not intended to be part of the data but if that were so then it ought to have been written that way so that others don't have to edit it. In any case the code above should work.

line1 = "GGCTTATTTAACGGGCAGATATACGCTGGGCAAATC ..." 

Answer 2

To convert that list to a character vector you can just go:

x <- strsplit(line1, "")
x <- x[[1]]

To make it a column of a df you can either go:

x <- as.data.frame(x)

Or just do it directly from the first line:

x <- as.data.frame(strsplit(line1, ""))

That'll give it an ugly column header which you can fix with

names(x)[1] <- 'whatever'

Or again directly in the one call:

x <- as.data.frame(strsplit(line1, ""), col.names = 'whatever')

Answer 3

The question seems to ask for the output of dput but this is seldom needed.

x <- strsplit(line1, "")[[1]]
dput(x)
#c("G", "G", "C", "T", "T", "A", "T", "T", "T", "A", "A", "C", 
#"G", "G", "G", "C", "A", "G", "A", "T", "A", "T", "A", "C", "G", 
#"C", "T", "G", "G", "G", "C", "A", "A", "A", "T", "C")

---

As for the question on how to get integers from the string, here is a way. The output are the ASCII codes for the letters in the original line1 string.

charToRaw(line1)
# [1] 47 47 43 54 54 41 54 54 54 41 41 43 47 47 47 43 41 47 41 54 41 54 41
#[24] 43 47 43 54 47 47 47 43 41 41 41 54 43

---

Data

line1 <- "GGCTTATTTAACGGGCAGATATACGCTGGGCAAATC"