R help - Mar 2018 - how to make row.names based on column1 with duplicated values

Dear All,
Suppose I have a dataframe like this with many thousands rows all with
different names:
data.frame(gene=c("a","b","c","d","c","d","c","f"),value=c(20,300,48,55,9,2,100,200)),

I want to set column "gene" as row.names, but there are duplicates (c,
d),
which I want to transform into this as row names: a, b, c-1, d-1, c-2, d-2,
c-3, f

Many thanks!

Stephen

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On Wed, 28 Feb 2018, Stephen HonKit Wong wrote:
> Dear All,
> Suppose I have a dataframe like this with many thousands rows all with
> different names:
>
data.frame(gene=c("a","b","c","d","c","d","c","f"),value=c(20,300,48,55,9,2,100,200)),
>
> I want to set column "gene" as row.names, but there are
duplicates (c, d),
> which I want to transform into this as row names: a, b, c-1, d-1, c-2, d-2,
> c-3, f
a) My reaction is that this doesn't actually sound like a very useful 
thing to do, so I caution you to beware of trying to accomplish too much 
with this capability... if it continues to be difficult to do what you 
want once you have these row names that appear nowhere else in your data, 
start looking for other ways to obtain the actual answers you want.

b) If your data frame is stored in `dta`, then you can do

rownames( dta ) <- make.names( dta$gene, unique = TRUE, sep="-" )

---------------------------------------------------------------------------
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Hi

You probably meant
make.unique( gene, sep="-" )
[1] "a"   "b"   "c"   "d"  
"c-1" "d-1" "c-2" "f"

I second your objection to such name tweeking.

Cheers
Petr
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Jeff
> Newmiller
> Sent: Thursday, March 1, 2018 9:13 AM
> To: Stephen HonKit Wong <stephen66 at gmail.com>
> Cc: r-help at r-project.org
> Subject: Re: [R] how to make row.names based on column1 with duplicated
> values
>
> On Wed, 28 Feb 2018, Stephen HonKit Wong wrote:
>
> > Dear All,
> > Suppose I have a dataframe like this with many thousands rows all with
> > different names:
> >
data.frame(gene=c("a","b","c","d","c","d","c","f"),value=c(20,300,48,5
> > 5,9,2,100,200)),
> >
> > I want to set column "gene" as row.names, but there are
duplicates (c,
> > d), which I want to transform into this as row names: a, b, c-1, d-1,
> > c-2, d-2, c-3, f
>
> a) My reaction is that this doesn't actually sound like a very useful
thing to do,
> so I caution you to beware of trying to accomplish too much with this
> capability... if it continues to be difficult to do what you want once you
have
> these row names that appear nowhere else in your data, start looking for
other
> ways to obtain the actual answers you want.
>
> b) If your data frame is stored in `dta`, then you can do
>
> rownames( dta ) <- make.names( dta$gene, unique = TRUE,
sep="-" )
>
> ---------------------------------------------------------------------------
> Jeff Newmiller                        The     .....       .....  Go Live...
> DCN:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#. 
Live Go...
>                                        Live:   OO#.. Dead: OO#..  Playing
> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> /Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
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You can do this with ave():

gene <-
c("a","b","c","d","c","d","c","f")
ave(gene, gene,
FUN=function(x)if(length(x)>1)paste(x,seq_along(x),sep="-")
else x)
# [1] "a"   "b"   "c-1" "d-1"
"c-2" "d-2" "c-3" "f"

You can probably speed it up a bit by pulling the paste() out of FUN
and doing it later.  It would be simpler if you put the '-N' after all
genes,
not just the ones that were not repeated.



Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Wed, Feb 28, 2018 at 10:18 PM, Stephen HonKit Wong <stephen66 at
gmail.com>
wrote:
> Dear All,
> Suppose I have a dataframe like this with many thousands rows all with
> different names:
>
data.frame(gene=c("a","b","c","d","c","d","c","f"),value=c(
> 20,300,48,55,9,2,100,200)),
>
> I want to set column "gene" as row.names, but there are
duplicates (c, d),
> which I want to transform into this as row names: a, b, c-1, d-1, c-2, d-2,
> c-3, f
>
> Many thanks!
>
> Stephen
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
>
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