On Nov 10, 2007 12:25 AM, affy snp <[EMAIL PROTECTED]> wrote:
> Hi Gabor,
>
> Thanks a lot!
>
> The header of the big file looks like as follows:
>
> probe_set
> WM_806_Signal_A
> WM_806_call
> WM_1716_Signal_A
> WM_1716_call
> ....
>
> I only need those columns with the header as like _Signal_A
>
> Can you suggest how to use sqldf?
>
sqlite requires that a single character separate the fields. Use sed or
other method to reduce multiple spaces to one space in the input
file and then try something like this:
library(sqldf)
source("http://sqldf.googlecode.com/svn/trunk/R/sqldf.R";)
# get headings
myfile <- file("myfile.dat")
stmt <- read.table(myfile, nr = 1, as.is = TRUE)
# assume any column with call in its name is to be eliminated
# and form select statement
stmt <- stmt[regexpr("call", stmt) < 0]
stmt <- paste("select", paste(stmt, collapse = ","), "from myfile")
# run it
myfile <- file("myfile.dat")
DF <- sqldf(stmt, file.format = list(sep = " "))
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