[R] reading in results from system(). There must be an easier way...
marc_schwartz at comcast.net
Fri Sep 12 18:58:23 CEST 2008
on 09/12/2008 11:34 AM Michael A. Gilchrist wrote:
> I am currently using R to run an external program and then read the
> results the external program sends to the stdout which are tsv data.
> When R reads the results in it converts it to to a list of strings which
> I then have to maniuplate with a whole slew of commands (which, figuring
> out how to do was a reall challenge for a newbie like myself)--see below.
> Here's the code I'm using. COMMAND runs the external program.
> rawInput= system(COMMAND,intern=TRUE);##read in tsv values
> rawInput = strsplit(rawInput, split="\t");##split elements w/in the
> ##of character strings by "\t"
> rawInput = unlist(rawInput); ##unlist, making it one long vector
> mode(rawInput)="double"; ##convert from strings to double
> finalInput = data.frame(t(matrix(rawInput, nrow=6))); ##convert
> Because I will be doing this 100,000 of times as part of an optimization
> problem, I am interested in learning a more efficient way of doing this
> Any suggestions would be appreciated.
> Thanks in advance.
Based upon the presumption that your incoming data are simple tab
delimited values in lines, no header record and where each line is to
end up as a single row in a data frame, you could use something like the
finalDF <- read.table(textConnection(system(COMMAND,intern = TRUE)),
sep = "\t", header = FALSE)
Alternatively, you could use scan() directly, then convert to a matrix:
finalMAT <- matrix(scan(textConnection(system(COMMAND,intern = TRUE)),
sep = "\t"),
nrow = 6)
These are untested of course, but should get you close, if not there.
See ?textConnection for the basic process of taking incoming data from a
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