Re: [R] Fwd: which is faster "for" or "apply"

2014-12-31 Thread Karim Mezhoud
Thanks, please find what I got: > str(getProfileData(cgds,GeneList, "stad_tcga_methylation_hm27","stad_tcga_methylation_hm27")) 'data.frame':48 obs. of 10 variables: $ ATM : num NA NA NA NA NA NA NA NA NA NA ... $ ATR : num NA NA NA NA NA NA NA NA NA NA ... $ DDR2 : num 0.714 0.857 0.

Re: [R] Fwd: which is faster "for" or "apply"

2014-12-31 Thread William Dunlap
> But this heterogeneity comes even with only supposed numeric data.frame > (gene expression). here an example > > ibrary(cgdsr) > GeneList <- c("DDR2", "HPGDS", "MS4A2","SSUH2","MLH1" ,"MSH2", "ATM" > ,"ATR", "MDC1" ,"PARP1") > cgds<-CGDS("http://www.cbioportal.org/public-portal/";) > > str(getPr

Re: [R] Fwd: which is faster "for" or "apply"

2014-12-31 Thread Karim Mezhoud
for both cidx <- !(sapply(df, is.numeric)) df[cidx] <- lapply(df[cidx], as.numeric) Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Wed, Dec 31, 2014 at 5:51 PM, Karim Mezhoud wrote: > Yes the last one this the best. But I need to test if returned data.frame

Re: [R] Fwd: which is faster "for" or "apply"

2014-12-31 Thread Karim Mezhoud
Yes the last one this the best. But I need to test if returned data.frame is with factor or character: cidx <- sapply(df, is.factor) or cidx <- sapply(df, is.character) Thanks Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Wed, Dec 31, 2014 at 5:24 PM, Karim

Re: [R] Fwd: which is faster "for" or "apply"

2014-12-31 Thread Karim Mezhoud
Concretely I request cbioportal through cgsdr package. Depending of Cases and Genetic profiles I receive in general data.frame with heterogeneous structure. The bad one if the returned data.frame is composed by numeric and character columns. in this case numeric columns are considered as factor. I

Re: [R] Fwd: which is faster "for" or "apply"

2014-12-31 Thread Karim Mezhoud
Many Many Many thanks! it is a demonstrative lesson. I need time to test all examples :) Thank you for your time and support. Happy and Healthy New Year Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Wed, Dec 31, 2014 at 2:38 PM, Martin Morgan wrote: > On 12

Re: [R] Fwd: which is faster "for" or "apply"

2014-12-31 Thread Martin Morgan
On 12/31/2014 12:22 AM, Karim Mezhoud wrote: Thanks, It seems for loop spends less time ;) with dim(DataFrame) [1] 338 70 For loop has user system elapsed 0.012 0.000 0.012 and apply has user system elapsed 0.020 0.000 0.021 The timings are so short that the answer in

[R] Fwd: which is faster "for" or "apply"

2014-12-31 Thread Karim Mezhoud
Thanks, It seems for loop spends less time ;) with dim(DataFrame) [1] 338 70 For loop has user system elapsed 0.012 0.000 0.012 and apply has user system elapsed 0.020 0.000 0.021 Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Wed, Dec 31