R help - Oct 2010 - vectorizing problem

Hello,

I have a two column dataframe that
has entries that look like this:

2315100       NR_024005,NR_024004,AK093685
2315106       DQ786314

and I want to change this to look like this:

2315100       NR_024005
2315100       NR_024004
2315100       AK093685
2315106       DQ786314

I can do this with the following "for" loop but the dataframe (GPL)
has ~140,000 rows and this takes about 15 minutes:


extGPL <- matrix(nrow=0,ncol=2)
for (i in 1:length(GPL[,2])){
       aa <- unlist(strsplit(as.character(GPL[i,2]),"\\,"))
       bb <- rep(as.numeric(as.character(GPL[i,1])), length(aa))
       cc <- matrix(c(bb,aa),ncol = 2)
       extGPL <- rbind(extGPL,cc)
}

Is there a way to vectorize this?

Thanks,

Dylan Miracle
University of Minnesota
GCD Department

Try this:

do.call(rbind.data.frame, mapply(cbind, DF$V1, strsplit(as.character(DF$V2),
",")))

On Mon, Oct 4, 2010 at 2:54 PM, Dylan Miracle
<dylan.miracle@gmail.com>wrote:
> Hello,
>
> I have a two column dataframe that
> has entries that look like this:
>
> 2315100       NR_024005,NR_024004,AK093685
> 2315106       DQ786314
>
> and I want to change this to look like this:
>
> 2315100       NR_024005
> 2315100       NR_024004
> 2315100       AK093685
> 2315106       DQ786314
>
> I can do this with the following "for" loop but the dataframe
(GPL)
> has ~140,000 rows and this takes about 15 minutes:
>
>
> extGPL <- matrix(nrow=0,ncol=2)
> for (i in 1:length(GPL[,2])){
>       aa <- unlist(strsplit(as.character(GPL[i,2]),"\\,"))
>       bb <- rep(as.numeric(as.character(GPL[i,1])), length(aa))
>       cc <- matrix(c(bb,aa),ncol = 2)
>       extGPL <- rbind(extGPL,cc)
> }
>
> Is there a way to vectorize this?
>
> Thanks,
>
> Dylan Miracle
> University of Minnesota
> GCD Department
>
> ______________________________________________
> R-help@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.
>


-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O

	[[alternative HTML version deleted]]

try this:

GPL <- data.frame(x = c(2315100, 2315106),
     y = c("NR_024005,NR_024004,AK093685", "DQ786314"))

sp <- strsplit(as.character(GPL$y), ",")
ni <- sapply(sp, length)
data.frame(x = rep(GPL$x, ni), y = unlist(sp))


I hope it helps.

Best,
Dimitris


On 10/4/2010 7:54 PM, Dylan Miracle wrote:
> Hello,
>
> I have a two column dataframe that
> has entries that look like this:
>
> 2315100       NR_024005,NR_024004,AK093685
> 2315106       DQ786314
>
> and I want to change this to look like this:
>
> 2315100       NR_024005
> 2315100       NR_024004
> 2315100       AK093685
> 2315106       DQ786314
>
> I can do this with the following "for" loop but the dataframe
(GPL)
> has ~140,000 rows and this takes about 15 minutes:
>
>
> extGPL<- matrix(nrow=0,ncol=2)
> for (i in 1:length(GPL[,2])){
>         aa<- unlist(strsplit(as.character(GPL[i,2]),"\\,"))
>         bb<- rep(as.numeric(as.character(GPL[i,1])), length(aa))
>         cc<- matrix(c(bb,aa),ncol = 2)
>         extGPL<- rbind(extGPL,cc)
> }
>
> Is there a way to vectorize this?
>
> Thanks,
>
> Dylan Miracle
> University of Minnesota
> GCD Department
>
> ______________________________________________
> 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.
>
-- 
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center

Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014
Web: http://www.erasmusmc.nl/biostatistiek/

On Mon, Oct 4, 2010 at 1:54 PM, Dylan Miracle <dylan.miracle at gmail.com>
wrote:
> Hello,
>
> I have a two column dataframe that
> has entries that look like this:
>
> 2315100 ? ? ? NR_024005,NR_024004,AK093685
> 2315106 ? ? ? DQ786314
>
> and I want to change this to look like this:
>
> 2315100 ? ? ? NR_024005
> 2315100 ? ? ? NR_024004
> 2315100 ? ? ? AK093685
> 2315106 ? ? ? DQ786314
>
> I can do this with the following "for" loop but the dataframe
(GPL)
> has ~140,000 rows and this takes about 15 minutes:
Try this assuming that the columns of GPL are character.  You may need
to use as.character first if they are factor:

library(reshape2)
V2 <- strsplit(GPL$V2, ",")
names(V2) <- GPL$V1
melt(V2)

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