How to transpose it in a fast way?
On Mar 7, 2013, at 01:18 , Yao He wrote:
Dear all:
I have a big data file of 60000 columns and 60000 rows like that:
AA AC AA AA .......AT
CC CC CT CT.......TC
..........................
.........................
I want to transpose it and the output is a new like that
AA CC ............
AC CC............
AA CT.............
AA CT.........
....................
....................
AT TC.............
The keypoint is I can't read it into R by read.table() because the
data is too large,so I try that:
c<-file("silygenotype.txt","r")
geno_t<-list()
repeat{
line<-readLines(c,n=1)
if (length(line)==0)break #end of file
line<-unlist(strsplit(line,"\t"))
geno_t<-cbind(geno_t,line)
}
write.table(geno_t,"xxx.txt")
It works but it is too slow ,how to optimize it???
As others have pointed out, that's a lot of data!
You seem to have the right idea: If you read the columns line by line there is nothing to transpose. A couple of points, though:
- The cbind() is a potential performance hit since it copies the list every time around. geno_t <- vector("list", 60000) and then
geno_t[[i]] <- <etc>
- You might use scan() instead of readLines, strsplit
- Perhaps consider the data type as you seem to be reading strings with 16 possible values (I suspect that R already optimizes string storage to make this point moot, though.)
Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com