I created a function that splits a string by ":" and takes the first element, which is the information I need from a vcf:
remove_semicolon = function(x){
newstr = strsplit(x,":")[[1]][1]
return(newstr)
}
I wish to apply it to every element of a data frame such as the following:
>rubbish
NS05 NS113 NS137
1 0/0:1 0/0:15 0/0:25
2 0/0:1 0/0:15 0/0:25
3 0/0:1 0/0:16 0/0:25
4 1/1:0,1:1:3:39,3,0 1/1:0,16:16:48:621,48,0 1/1:0,26:26:78:969,78,0
5 0/0:1 0/0:16 0/0:29
So that for rubbish[1,1] the desired output is "0/0", for rubbish[4,1] "1/1" etc, with the matrix/data frame structure left intact. However,
rubbish[]=lapply(rubbish,remove_semicolon)
returns:
> rubbish
NS05 NS113 NS137
1 0/0 0/0 0/0
2 0/0 0/0 0/0
3 0/0 0/0 0/0
4 0/0 0/0 0/0
5 0/0 0/0 0/0
even though, in contrast,
sapply(rubbish[,1],remove_semicolon)
returns what I want, i.e. a vector 0/0, 0/0, 0/0, 1/1, 0/0 rather than all 0/0:
0/0:1 0/0:1 0/0:1 1/1:0,1:1:3:39,3,0
"0/0" "0/0" "0/0" "1/1"
0/0:1
"0/0"
What am I doing incorrectly when implement lapply? Shouldn't it just apply the remove_semicolon function to every element of rubbish in the same way that sapply does it for every element of a column vector?
Using apply(., MARGIN = 1:2, .) seems to work:
rubbish[] <- apply(rubbish, 1:2, remove_semicolon)
NS05 NS113 NS137
1 0/0 0/0 0/0
2 0/0 0/0 0/0
3 0/0 0/0 0/0
4 1/1 1/1 1/1
5 0/0 0/0 0/0
If you look at the output of lapply(rubbish, remove_semicolon) (before assigning it back to the data frame) you'll see that each element of the output is a length-1 vector (which then gets replicated to fill the column). This happens because remove_semicolon isn't vectorized.
This would work with lapply():
rs2 <- function(x) {
newstr <- strsplit(x, ":")
return(sapply(newstr, head, 1))
}
lapply(rubbish, rs2)
Another alternative would be to use gsub() (or stringr::str_extract) with a regular expression, e.g.
rs3 <- function(x) gsub("^([^:]+):.*$", "\\1", x)
(it does admittedly look a little like magic)
rubbish <- read.table(header = TRUE, text = "
NS05 NS113 NS137
0/0:1 0/0:15 0/0:25
0/0:1 0/0:15 0/0:25
0/0:1 0/0:16 0/0:25
1/1:0,1:1:3:39,3,0 1/1:0,16:16:48:621,48,0 1/1:0,26:26:78:969,78,0
0/0:1 0/0:16 0/0:29
")