Re: [R] R console not echoing input

Hi Mik. Likely you executed sink(...) to redirect output somewhere. You undo that with sink(). You can compute how many such sinks are in effect (they stack) using sink.number(), but you probably won't be able to see the output, so that's more useful in something like while (sink.number()

[R] R console not echoing input

I have a weird problem running R.app 3.3.2 under Mac OS X 10.10.5. I was trying to interrupt a command line using various Control codes until I discovered that “Esc” is the escape key. (Makes sense!) Now I find that while I can enter new commands to R, they no longer echo back, so I cannot see

Re: [R] reshaping the data

Thanks a lot gentlemen, and particularly Petr -- the R code you did share helped tremendously ;) On Mon, Jul 3, 2017 at 2:53 AM, PIKAL Petr wrote: > Hi > > Do you want something like > > dcast(test, Sample~Gene, fun=function(x) paste(x, collapse=",")) > > or > > dcast(test, Sample~Gene, fun=func

Re: [R] R memory limits on table(x, y) (and bigtabulate)

Yes. Table and matrix size limits are set by the max.integer size which is fixed at what can be represented with 4 bytes. David Sent from my iPhone > On Jul 3, 2017, at 8:04 AM, Bert Gunter wrote: > > Sorry, don't know enough to give you trustworthy answers, but I can > say that crashes due

Re: [R] R memory limits on table(x, y) (and bigtabulate)

Sorry, don't know enough to give you trustworthy answers, but I can say that crashes due to (or linked to) packages should usually be reported to the package maintainer, who can be found by the ?maintainer function. That person may not monitor this list. Cheers, Bert Bert Gunter "The trouble w

[R] R memory limits on table(x, y) (and bigtabulate)

I have two character vectors x and y that have the following characteristics: length(x) # same as length(y) # 872099 length(unique(x)) # 47740 length(unique(y)) # 52478 I need to crosstabulate them, which would lead to a table with 47740*52478 # 2505299720 cells, which is more than 2^31 # 2

Re: [R] reshaping the data

Hi Do you want something like dcast(test, Sample~Gene, fun=function(x) paste(x, collapse=",")) or dcast(test, Sample~Gene, fun=function(x) sum(as.numeric(x))) 1 means INDEL, 2 means SNV and three means both Cheers Petr > -Original Message- > From: R-help [mailto:r-help-boun...@r-pro

[R] Calculating cumulative lengths of hierarchical topology

Hello All, I need to calculate cumulative lengths along a hierarchical network topology (it's a representation of a tree). I can roll my own, but thought that there might be a package out there that would handle hierarchical network topology functions such as this nicely (and that might brin

Re: [R] reshaping the data

Hi Bogdan, If you want something like this: 22M 17M 11M AEBP1 SNV SNV NA ATR INDEL NA NA ATR SNV NANA BTKNA NA SNV BTK NA NA INDEL You're in trouble with repeated row names. Same with column names i

Re: [R] Packages for Learning Algorithm Independent Branch and Bound for Feature Selection

Quoting Alex Byrley : See, I have built my own genetic algorithm already and tested it on this problem. I have a solution, but due to the heuristic nature of GA, I cannot guarantee that it is the optimal subset. If I was simply doing this for a company project, you are spot on with the type of

[R] reshaping the data

Dear all, I would appreciate please a piece of help regarding the use of acast/dcast functions in reshape2 package. Specifically, I'm working with a data frame, that has information about SAMPLE, GENE, and TYPE of MUTATION (as shown below): SampleGene Type 22M AEBP1 SNV 17M AE