You are spending most of the time in the loop accessing the dataframe. Put
the data you want out to a vector and then process that:
> x <- read.table(textConnection(" Row.ID AgilentProbe GeneSymbol
GeneID Exons AgilentStart first.geneid first.exon last.geneid last.exon
+ 8 1348 A_23_P116898 A2M 2 34 9112685
TRUE TRUE TRUE TRUE
+ 62 19410 A_23_P95594 NAT1 9 4 18124656
TRUE TRUE TRUE TRUE
+ 39 10323 A_23_P31798 NAT2 10 2 18302422
TRUE TRUE TRUE TRUE
+ 21 5353 A_23_P162918 SERPINA3 12 5 94150936
TRUE TRUE FALSE FALSE
+ 22 9999 A_23_P162913 SERPINA3 12 5 94150800
FALSE FALSE FALSE FALSE
+ 98 29990 A_32_P151937 SERPINA3 12 5 94150720
FALSE FALSE FALSE TRUE
+ 33 9516 A_23_P2920 SERPINA3 12 7 94158435
FALSE TRUE FALSE TRUE
+ 96 29595 A_32_P124727 SERPINA3 12 8 94160018
FALSE TRUE TRUE TRUE
+ 57 18176 A_23_P80570 AADAC 13 5 153028473
TRUE TRUE TRUE TRUE
+ 46 16139 A_23_P56529 AAMP 14 9 218838396
TRUE TRUE TRUE TRUE
+ 18 4438 A_23_P152527 AANAT 15 7 71976911
TRUE TRUE TRUE TRUE
+ 69 21321 A_24_P172990 AARS 16 18 68845436
TRUE TRUE TRUE TRUE
+ 82 24747 A_24_P330684 ABAT 18 17 8780872
TRUE TRUE FALSE TRUE"), header=TRUE, as.is=TRUE)
> closeAllConnections()
> # create character string
> p1 <- x$AgilentProbe
> test <- x$first.exon
> for (i in seq_along(p1)){
+ if (!test[i]) p1[i] <- paste(p1[i-1], p1[i], sep=',')
+ }
> cbind(p1)
p1
[1,] "A_23_P116898"
[2,] "A_23_P95594"
[3,] "A_23_P31798"
[4,] "A_23_P162918"
[5,] "A_23_P162918,A_23_P162913"
[6,] "A_23_P162918,A_23_P162913,A_32_P151937"
[7,] "A_23_P2920"
[8,] "A_32_P124727"
[9,] "A_23_P80570"
[10,] "A_23_P56529"
[11,] "A_23_P152527"
[12,] "A_24_P172990"
[13,] "A_24_P330684"
>
On Tue, May 11, 2010 at 12:33 PM, jim holtman <jholt...@gmail.com> wrote:
> Instead of looping on each row, try the following
>
> p1 <- as.character(aga$AP)
> # skew by one on the paste
> p1 <- ifelse(aga2$first.exon, p1, paste(c("", tail(ags, -1)), aga2$AP,
> sep=','))
>
> ags <- as.character(aga$AS)
> ags <- ifelse(aga2$first.exon, ags, paste(c("", tail(ags, -1)), aga2$AS,
> sep=',')
>
> On Tue, May 11, 2010 at 12:17 PM, Mark Lamias <mlam...@yahoo.com> wrote:
>
>> R-users,
>>
>> I have the following piece of code which I am trying to run on a dataframe
>> (aga2) with about a half million records. While the code works, it is
>> extremely slow. I've read some of the help archives indicating that I
>> should allocate space to the p1 and ags1 vectors, which I have done, but
>> this doesn't seem to improve speed much. Would anyone be able to provide me
>> with advice on how I might be able to speed this up?
>>
>>
>> p1 <- character(dim(aga2)[1])
>> ags <- character(dim(aga2)[1])
>> for (i in 1:dim(aga2)[1])
>> {
>> if (aga2$first.exon[i]==TRUE)
>> {
>> p1[i]<-as.character(aga2[i, "AP"])
>> ags[i]<-as.character(aga2[i, "AS"])
>>
>> }
>> else
>> {
>> p1[i]<-paste(p1[i-1], aga2[i, "AP"], sep=",")
>> ags[i]<-paste(ags[i-1], aga2[i, "AS"], sep=",")
>> }
>> }
>>
>> Thanks.
>>
>> --Mark Lamias
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>>
>> ______________________________________________
>> 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<http://www.r-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
>
> --
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
>
> What is the problem that you are trying to solve?
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
