Question

Whenever I read in a file using read.csv() with option header=T, the headers change in weird (but predictable) ways. A header name which ought to read "P(A<B)" becomes "P.A.B.", for instance:

> # when header=F:
> myfile1 <- read.csv(fullpath,sep="\t",header=F,nrow=3)
> myfile1
     V1    V2     V3
1    ID  Name P(A>B)
2 AB001 Alice  0.997
3 AB002   Bob  0.497
>
> # When header=T:
> myfile2 <- read.csv(fullpath,sep="\t",header=T,nrow=3)
> myfile2
     ID    Name P.A.B.
1 AB001   Alice  0.997
2 AB002     Bob  0.497
3 AB003 Charles  0.732

I tried to fix it like this, but it didn’t work:

> names(myfile2) <- myfile1[1,]
> myfile2
      3       3     3
1 AB001   Alice 0.997
2 AB002     Bob 0.497
3 AB003 Charles 0.732

So then I tried to use sub() to write a function that would take any vector "arbitrary.lengths.here." and return a vector "arbitrary(lengths>here)", but I didn’t really get anywhere, and I started to suspect that I was making this problem more complicated than it had to be.

How would you deal with this problem of headers? Was I on the right track with sub()?

Answer 1

Set check.names=FALSE in read.csv()

read.csv(fullpath,sep="\t", header=FALSE, nrow=3, check.names=FALSE)

From the help for ?read.csv:

check.names

logical. If TRUE then the names of the variables in the data frame are checked to ensure that they are syntactically valid variable names. If necessary they are adjusted (by make.names) so that they are, and also to ensure that there are no duplicates.