[R] Selecting columns whose names contain "mutated" except when they also contain "non" or "un"

[Paul Miller]

Hi Bert,

Yes, code like:

x <- names(yourdataframe)
grepl("muta",x) & !grepl("nonmuta|unmuta",x)

works perfectly.

Thanks very much for your help.

Paul




--- On Mon, 4/23/12, Bert Gunter <gunter.berton at gene.com> wrote:

> From: Bert Gunter <gunter.berton at gene.com>
> Subject: Re: [R] Selecting columns whose names contain "mutated" except when they also contain "non" or "un"
> To: "Paul Miller" <pjmiller_57 at yahoo.com>
> Cc: "David Winsemius" <dwinsemius at comcast.net>, r-help at r-project.org
> Received: Monday, April 23, 2012, 12:15 PM
> But maybe ... (see below)
> -- Bert
> 
> On Mon, Apr 23, 2012 at 9:25 AM, Paul Miller <pjmiller_57 at yahoo.com>
> wrote:
> > Hello Dr. Winsemius,
> >
> > Unfortunately, I also have terms like "krasmutated". So
> simply selecting words that start with "muta" won't work in
> this case.
> >
> > Thanks,
> >
> > Paul
> >
> >
> > --- On Mon, 4/23/12, David Winsemius <dwinsemius at comcast.net>
> wrote:
> >
> >> From: David Winsemius <dwinsemius at comcast.net>
> >> Subject: Re: [R] Selecting columns whose names
> contain "mutated" except when they also contain "non" or
> "un"
> >> To: "Paul Miller" <pjmiller_57 at yahoo.com>
> >> Cc: r-help at r-project.org
> >> Received: Monday, April 23, 2012, 11:16 AM
> >>
> >> On Apr 23, 2012, at 12:10 PM, Paul Miller wrote:
> >>
> >> > Hello All,
> >> >
> >> > Started out awhile ago trying to select
> columns in a
> >> dataframe whose names contain some variation of the
> word
> >> "mutant" using code like:
> >> >
> >> > names(KRASyn)[grep("muta", names(KRASyn))]
> >> >
> >> > The idea then would be to add together the
> various
> >> columns using code like:
> >> >
> >> > KRASyn$Mutant_comb <-
> rowSums(KRASyn[grep("muta",
> >> names(KRASyn))])
> >> >
> >> > What I discovered though, is that this selects
> columns
> >> like "nonmutated" and "unmutated" as well as
> columns like
> >> "mutated", "mutation", and "mutational".
> >> >
> >> > So I'd like to know how to select columns that
> have
> >> some variation of the word "mutant" without the
> "non" or the
> >> "un". I've been looking around for an example of
> how to do
> >> that but haven't found anything yet.
> 
> If this **is** a complete specification then wouldn't
> simply:
> 
> x <- names(yourdataframe)
>  grepl("muta",x) & !grepl("nonmuta|unmuta",x)
> 
> do it?
> 
> e.g.
> > x <-
> c("nonmutated","unmutated","mutation","mutated","krasmutated")
> > grepl("muta",x) & !grepl("nonmuta|unmuta",x)
> [1] FALSE FALSE  TRUE  TRUE  TRUE
> 
> >> >
> >> > Can anyone show me how to select the columns I
> need?
> >>
> >> If you want only columns whose names _begin_ with
> "muta"
> >> then add the "^" character at the beginning of
> your
> >> pattern:
> >>
> >> names(KRASyn)[grep("^muta", names(KRASyn))]
> >>
> >> (This should be explained on the ?regex page.)
> >>
> >> --
> >> David Winsemius, MD
> >> West Hartford, CT
> >>
> >>
> >
> > ______________________________________________
> > R-help at r-project.org
> mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained,
> reproducible code.
> 
> 
> 
> -- 
> 
> Bert Gunter
> Genentech Nonclinical Biostatistics
> 
> Internal Contact Info:
> Phone: 467-7374
> Website:
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>