R help - Dec 2009 - How to exclude lines that match certain regex when using read.table?

I'm thinking of using external program 'grep' and pipe() to do so.
But
I'm wondering if there is a more efficient way to do so purely in R

pengyu.ut wrote:
> 
> I'm thinking of using external program 'grep' and pipe() to do
so. But
> I'm wondering if there is a more efficient way to do so purely in R
> 
I would just suck the whole table in using read.table(), locate the lines
that I don't want using apply() and grepl() and then reduce the data set:

  dataSet <- read.table( "someData.txt" )

  dataToDrop <- apply( dataSet, 1, function( row ){

    return(
      any( grepl( "regex", row ) )
    )

  })

  dataSet <- subset( dataSet, !dataToDrop )

Since this solution executes entirely in R without resorting to system()
calls, it should be portable between platforms.

-Charlie
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Using grep in a pipeline is pretty fast so if that is workable that is
probably the way to go; however, one other possibility is to use
read.csv.sql from the sqldf package.   read.csv.sql allows you to specify an
sql statement that it will use to filter the data. It reads the data into a
temporary sqlite database (which it automatically sets up for you and uses
sqlite, not R, to do that) and then applies the sql statement reading the
presumably much smaller result into R and finally automatically destroy the
temporary database. Whether that is faster or slower than the alternatives
could easily be tested as read.csv.sql takes only one line of code.  See the
examples at http://sqldf.googlecode.com

On Thu, Dec 3, 2009 at 9:34 PM, Peng Yu <pengyu.ut@gmail.com> wrote:
> I'm thinking of using external program 'grep' and pipe() to do
so. But
> I'm wondering if there is a more efficient way to do so purely in R
>
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