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...;), I=c(100,300,400)) MN<-as.data.frame(matrix(NA,nrow=length(N[,1]),ncol=length(M[,1]))) names(MN)<-M[,1] rownames(MN)<-N[,1] C[,1]<-as.character(C[,1]) C[,2]<-as.character(C[,2]) for(row in 1:dim(C)[1]) MN[C[row,1],C[row,2]]<-C[row,3] Jim On Tue, Jun 6, 2017 at 3:51 PM, Bogdan Tanasa <tanasa at gmail.com> wrote: > Dear Bert, > > thank you for your response. here it is the piece of R code : given 3 data > frames below --- > > N <- data.frame(N=c("n1","n2","n3","n4")) > > M <- data.frame(M=c("m1&quot...

...). > > -- Bert > Bert Gunter > > "The trouble with having an open mind is that people keep coming along > and sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Mon, Jun 5, 2017 at 6:45 PM, Bogdan Tanasa <tanasa at gmail.com> wrote: > > Dear all, > > > > please could you advise on the R code I could use in order to do the > > following operation : > > > > a. -- I have 2 lists of "genome coordinates" : a list is composed by > > numbers that...

...ame" ------------------------------------- David L Carlson Department of Anthropology Texas A&M University College Station, TX 77840-4352 -----Original Message----- From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Jim Lemon Sent: Tuesday, June 6, 2017 6:02 AM To: Bogdan Tanasa <tanasa at gmail.com>; r-help mailing list <r-help at r-project.org> Subject: Re: [R] integrating 2 lists and a data frame in R Hi Bogdan, Kinda messy, but: N <- data.frame(N=c("n1","n2","n3","n4")) M <- data.frame(M=c("m1",&quot...

...,2:1])] <- C$I ## matrix indexing res Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Tue, Jun 6, 2017 at 7:46 AM, Bogdan Tanasa <tanasa at gmail.com> wrote: > Thank you David. Using xtabs operation simplifies the code very much, many > thanks ;) > > On Tue, Jun 6, 2017 at 7:44 AM, David Winsemius <dwinsemius at comcast.net> > wrote: > >> >> > On Jun 6, 2017, at 4:01 AM, Jim Lemon...

...CMatrix" n m n1 n2 n3 n4 m1 100 300 . . m3 . . 400 . m4 . . . . m5 . . . 0 (In the example I forgot to repeat the lines that augmented the factor levels so m2 is not seen. -- Davod > > > Jim > > On Tue, Jun 6, 2017 at 3:51 PM, Bogdan Tanasa <tanasa at gmail.com> wrote: >> Dear Bert, >> >> thank you for your response. here it is the piece of R code : given 3 data >> frames below --- >> >> N <- data.frame(N=c("n1","n2","n3","n4")) >> >> M...

...error message. (I am not posting the error message, because the R script I wrote works fine when it is run from a regular terminal ..) Please may I ask, how do you usually submit the R scripts with command line arguments to PBS HPC schedulers ? qsub -d $PWD -l nodes=1:ppn=4 -l vmem=10gb -m bea -M tanasa at gmail.com \ -v TUMOR="tumor.bam",GERMLINE="germline.bam",CHR="chr22" \ -e script.efile.chr22 \ -o script.ofile.chr22 \ script.R Thank you very very much ! -- bogdan [[alternative HTML version deleted]]

Hi, please could you recommend a R package that computes a 2 sample z-test ? thanks, Bogdan [[alternative HTML version deleted]]

...m3 . . 400 . > m4 . . . . > m5 . . . 0 > > (In the example I forgot to repeat the lines that augmented the factor > levels so m2 is not seen. > > -- > Davod > > > > > > Jim > > > > On Tue, Jun 6, 2017 at 3:51 PM, Bogdan Tanasa <tanasa at gmail.com> wrote: > >> Dear Bert, > >> > >> thank you for your response. here it is the piece of R code : given 3 > data > >> frames below --- > >> > >> N <- data.frame(N=c("n1","n2","n3",&quo...

...possibly different access credentials than your usual interactive terminal. A thorough reading of the "Installation and Administration Guide" and some study of your HPC documentation are in order. -- Sent from my phone. Please excuse my brevity. On July 11, 2017 5:25:20 PM PDT, Bogdan Tanasa <tanasa at gmail.com> wrote: >Dear all, > >please could you advise me on the following : I've written a R script >that >reads 3 arguments from the command line, i.e. : > >" args <- commandArgs(TRUE) >TUMOR <- args[1] >GERMLINE <- args[2] >CHR &l...

...ccess credentials than your usual interactive terminal. A thorough reading of the "Installation and Administration Guide" and some study of your HPC documentation are in order. > -- > Sent from my phone. Please excuse my brevity. > > On July 11, 2017 5:25:20 PM PDT, Bogdan Tanasa <tanasa at gmail.com> wrote: >> Dear all, >> >> please could you advise me on the following : I've written a R script >> that >> reads 3 arguments from the command line, i.e. : >> >> " args <- commandArgs(TRUE) >> TUMOR <- args[...

...es C look ilike? (You should know this by now). -- Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Mon, Jun 5, 2017 at 6:45 PM, Bogdan Tanasa <tanasa at gmail.com> wrote: > Dear all, > > please could you advise on the R code I could use in order to do the > following operation : > > a. -- I have 2 lists of "genome coordinates" : a list is composed by > numbers that represent genome coordinates; >...

Hi, and my apologies for the following very naive question : I would like to read a column of numbers in R and plot a histogram. eg : x<-read.table("txSTART"); y<-as.numeric(x); and I do obtain the error : Error: (list) object cannot be coerced to type 'double'. Please could you let me know the way to fix it. thanks, bogdan <r-help@r-project.org> [[alternative

Dear all, please could you advise on the R code I could use in order to do the following operation : a. -- I have 2 lists of "genome coordinates" : a list is composed by numbers that represent genome coordinates; let's say list N : n1 n2 n3 n4 and a list M: m1 m2 m3 m4 m5 2 -- and a data frame C, where for some pairs of coordinates (n,m) from the lists above, we have a

...in multgenes) df.sample.gene<-rbind(df.sample.gene,dup_row(df.sample.gene[multgene,])) df.sample.gene<-df.sample.gene[-multgenes,] df.sample.gene I added a second line with multiple genes to make sure that it would work with more than one line. Jim On Wed, Aug 23, 2017 at 9:57 AM, Bogdan Tanasa <tanasa at gmail.com> wrote: > I would appreciate please a suggestion on how to do the following : > > i'm working with a dataframe in R that contains in a specific column > multiple gene names, eg : > >> df.sample.gene[15:20,2:8] > Chr Start End Ref...

I would appreciate please a suggestion on how to do the following : i'm working with a dataframe in R that contains in a specific column multiple gene names, eg : > df.sample.gene[15:20,2:8] Chr Start End Ref Alt Func.refGene Gene.refGene284 chr2 16080996 16080996 C T ncRNA_exonic GACAT3448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191,LOC100499194465

...ple.gene,dup_row(df.sample.gene[multgene,])) > df.sample.gene<-df.sample.gene[-multgenes,] > df.sample.gene > > I added a second line with multiple genes to make sure that it would > work with more than one line. > > Jim > > > On Wed, Aug 23, 2017 at 9:57 AM, Bogdan Tanasa <tanasa at gmail.com> wrote: >> I would appreciate please a suggestion on how to do the following : >> >> i'm working with a dataframe in R that contains in a specific column >> multiple gene names, eg : >> >>> df.sample.gene[15:20,2:8] >>...

Hi everyone. I installed affylmGUI and oneChannelGUI package on R 2.7.1 with the latest version of BioC. After I start R, I do get an error that says "Error in loadNamespace(name) : there is no package called 'affylmGUI'" and a pop-up window with a message "fatal error : unable to restore saved data in .Rdata". I would really appreciate your suggestions on how to fix

Dear all, would appreciate a suggestion about the following situation : I am running a script in R, and shall i execute it in the terminal, step by step, it works fine. however, if i do source ("script.R"), it does not complete and I am getting the error : "Can only modify plain character vectors." what may go wrong ? thank you for your help, -- bogdan [[alternative HTML

Dear all, please could you suggest any R functions or packages (or external programs), that a. take as input a large number (> 10 000) of short 20-30 nt sequences, and do sequence assembly, to reconstruct larger (extended) 30-50 sequences ? b. take as input a larger number of sequences (100 000 - 1 mil) and cluster these sequences in distinct classes based on the sequence similarity ?

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): Sample Gene Type 22M AEBP1 SNV 17M AEBP1 SNV 22M ATR INDEL 22M ATR SNV 11M BTK SNV 11M BTK