This is very helpful. Thanks for explaining it. I'm clearly going to need to improve my understanding of regular expressions. Currently busy trying to figure out Sweave and knitr though.
> From: Greg Snow <
[hidden email]>
> Subject: Re: [R] Selecting columns whose names contain "mutated" except when they also contain "non" or "un"
> To: "Paul Miller" <
[hidden email]>
> Cc:
[hidden email]
> Received: Thursday, April 26, 2012, 1:55 PM
> Sorry I took so long getting back to
> this, but the paying job needs to
> take priority.
>
> The regular expression "(?<!un)(?<!non)muta"
> looks for a string that
> matches "muta" then looks at the characters immediately
> before it to
> see if they match either "un" or "non" in which case it
> makes it a not
> match. More specifically the regular expression engine
> steps through
> the string and at each point tries the match, so at a given
> point it
> will first see if "un" is before that point, if it is then
> this point
> can't match and it moves the checking point, if it is not
> "un" then it
> moves to the next negative look behind and sees if "non" is
> just
> before the point. If neither "un" or "non" are just
> before the point
> then it starts matching characters after the point to see if
> they
> match "muta".
>
> So the next pattern is "(?!muta)non|un", the (?!muta) is a
> negative
> look ahead which starts at the point and checks forward to
> see that
> the next characters are not "muta" (but does not include
> them in the
> match), in this case it is a no-op because you are saying
> that you
> want to match at a point where the next characters are not
> "muta" but
> are "non" and since the next set of characters cannot
> be both this is
> the same as just matching "non", also you need to be aware
> of the
> operator precedence, in that pattern the (?!muta) part only
> applied to
> the "non", not the "un".
>
> To match "nonmuta" or "unmuta" a simple pattern would just
> be
> "(non|un)muta" or "(no|u)nmuta". You could use the
> positive
> lookbehind (you would still need an "or"), but it would be
> overkill
> for a grep command. The difference in the positive
> look ahead/behind
> is more important for replacing where the look ahead/behind
> is needed
> for the match to happen, but is not captured as part of the
> match to
> be replaced.
>
>
>
> On Tue, Apr 24, 2012 at 7:40 AM, Paul Miller <
[hidden email]>
> wrote:
> > Hi Greg,
> >
> > This is quite helpful. Not so good yet with regular
> expressions in general or Perl-like regular expressions.
> Found the help page though, and think I was able to
> determine how the code works as well as how I would select
> only instances where "muta" is preceeded by either "non" or
> "un".
> >
> >> (tmp <-
> c('mutation','nonmutated','unmutated','verymutated','other'))
> > [1] "mutation" "nonmutated" "unmutated"
> "verymutated" "other"
> >
> >> grep("(?<!un)(?<!non)muta", tmp, perl=TRUE)
> > [1] 1 4
> >
> >> grep("(?!muta)non|un", tmp, perl=TRUE)
> > [1] 2 3
> >
> > Did I get the second grep right?
> >
> > If so, do you have any sense of why it seems to fail
> when I apply it to my data?
> >
> >> KRASyn$NonMutant_comb <-
> rowSums(KRASyn[grep("(?!muta)non|un", names(KRASyn),
> perl=TRUE)])
> >
> > Error in rowSums(KRASyn[grep("(?!muta)non|un",
> names(KRASyn), perl = TRUE)]) :
> > 'x' must be numeric
> >
> > Thanks,
> >
> > Paul
> >
>
>
>
> --
> Gregory (Greg) L. Snow Ph.D.
>
[hidden email]
>
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