similar to: Trouble obtaining results from a loop

#Hello, #I have would like to paste a single column of a matrix # in pair wise fashion with other columns based upon # even and odd column numbers. # I can do it in a very clunky fashion and I know there # must be a better way. below is a sample matrix and my extremely # clunky code that gets the job done for a small matrix, but i plan to # do this on a much grander scale. any help would be very

# Hello, # I have a list with 6 categories and with different numbers of rows. # I would like to change each of them into a unique data frame in order to match # values with other data frames and perform some calculations. # Or I could make each category or list element have the same number of rows and create one large data.frame. # below is a creation of a sample list # I apologize for the

Bottom Line Up Front: How does one reshape genetic data from long to wide? I currently have a lot of data. About 180 individuals (some probands/patients, some parents, rare siblings) and SNP data from 6000 loci on each. The standard formats seem to be something along the lines of Famid, pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2, locus2Allele1, locus2Allele2, etc In other

Hello, I am working with a matrix of multilocus genotypes for ~180 individual snail samples, with substantial missing data. I am trying to calculate the pairwise genetic distance between individuals using the stats package 'dist' function, using euclidean distance. I took a subset of this dataset (3 samples x 3 loci) to test how euclidean distance is calculated: 3x3 subset used

Hello All, Once again thanks for all of the help to date. I am climbing my R learning curve. I've got a few more questions that I hope I can get some guidance on though. I am not sure whether the etiquette is to break up multiple questions or not but I'll keep them together here for now as it may help put the questions in context despite the fact that the post may get a little long.

# Hello # I have a question regarding pairwise calculations of a matrix using a "for-loop." # Below I have a matrix "X" with 8 columns. These are Genotypic data so Column1 & Column2 is # a unit, Column3 & Column4 is a unit, Column5 & Column6 is a unit, and Coulmn7 & 8 is a unit. # I have a loop designed to calculate the number of times an individual in

Hello, I have two data frames, X and Y, with two columns each and different numbers of rows. # creation of data frame X Loc1.alleles <- c(1,5,6,7,8) Loc1.Freq <- c(0.35, 0.15, 0.05, 0.10, 0.35) Loc1 <- cbind( Loc1.alleles,Loc1.Freq) X <- data.frame(Loc1) #creation of data frame Y Loc2.alleles <- c(1,4,6,8) Loc2.Freq <- c(0.35, 0.35,

# Hello # I have a question regarding pairwise calculations of a matrix using a "for-loop." # Below I have a matrix "X" with 8 columns. These are genotypic data so Column1 & Column2 is # a unit, Column3 & Column4 is a unit, Column5 & Column6 is a unit, and Coulmn7 & 8 is a unit. # I have a loop designed to calculate the number of times an individual in

#Hello, #I have three data frames, X,Y and Z with two columns each and different numbers of rows. # creation of data frame X X.alleles <- c(1,5,6,7,8) X.Freq <- c(0.35, 0.15, 0.05 , 0.10, 0.35) Loc1 <- cbind( X.alleles,X.Freq) X <- data.frame(Loc1) #creation of data frame Y Y.alleles <- c(1,4,6,8) Y.Freq <- c(0.35, 0.35, 0.10, 0.20 )

Hello, I am having really hard time finding a good article about simulating genotypes of cases and controls at a disease locus using R. if you guys can point me or guide me where i can find more information, it will be helpful. thanks, Claire -- View this message in context: http://www.nabble.com/genotypes-simulation-tp17065607p17065607.html Sent from the R help mailing list archive at

#Hello, # I have a question about the addition of values in specific columns and rows of a Data frame. # Below I have created two data frames, X.df and "Y.df". ## creation of X.df data frame X<- matrix(0,16,3) X.df<-data.frame(X) X.df[,1] <- c(1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4) X.df[,2] <- c(1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4) names(X.df)[1]<-"L(A)a(i)"

Hi All, I have a problem trying to get a set of columns recognised as a list and can't work out how to do it despite trawling through the mailing list archives, and docs. A short example... to.convert <- NULL n <- 6 for(x in 1:n){ to.convert <- paste(to.convert, paste((2 * x) -1, (2 * x), sep=":"), sep=",") } to.convert <- gsub("^,", "",

Hello R-help community, I have another question about filtering datasets. Please consider the following "toy" data matrix example, called "x" for simplicity. There are 20 different individuals ("ID"), with information about the alleles (A,T, G, C) at six different loci ("Locus1" - "Locus6") for each of these 20 individuals. At any single locus

I am about one step away from heaven on earth. I think only one step! I am using dgc.genetics to run a TDT test on thousands of genetic loci. I have learnt (through the help of others on this mailing list) to send the complex output to useful data frames which in turn allow me to look at the big picture and screen the thousands of loci. Resultdt<-lapply(PGWide[,240:290], tdt) the above

I am using dgc.genetics to perform TDT analysis on SNP data from a cohort of trios. I now have a file with about 6008 variables. The first few variables related to the pedigree data such as the pedigree ID the person ID etc. Thereafter each variable is a specific locus or marker. The variables are named by a pattern such as "Genotype.nnnnn" with nnnnn corresponding to a number which

Hi , is it possible to calculate ld-measures D, D', r and perhaps corresponding p-values with r IF THE PHASE IS KNOWN? The genetics - package provides the LD function only for ambigious phase. Thank you very much Bettina Kulle

Dear all, I am running qtl mapping. I have 75 RI lines with some residual heterogeneous loci. The loci are code A, B or H(heterogeneous). Questions: 1) R/qtl determine the data is F2 intercross. 2) Warning message about strange genotype pattern > library(qtl) > dat=read.cross("csv", file="rqtl_trt.csv") --Read the following data: 75 individuals

Hi all - I am NEW to R and NEW to any type of programming. I am making heatmaps using the heatmap.2 function within gplots package. At present, when the heatmap is plotted it uses the row identifiers as 1,2,3,4...etc. However, I much rather use my own labels. I was told my another well-versed R programmer to use the follow script: x<-as.matrix(test1[,-1]) ## skip column 1 rownames(x)<-

Hi. I was wondering if anyone might have some suggestions about how I can overcome a problem of "iteration limit reached without convergence" when fitting a mixed effects model. In this study: Outcome is a measure of heart action Age is continuous (in weeks) Gender is Male or Female (0 or 1) Genotype is Wild type or knockout (0 or 1) Animal is the Animal ID as a factor

Hi, I am conducting an association analysis of genotype and a phenotype such as cholesterol level as an outcome and the genotype as a regressor using multiple linear regression. There are 3 possibilities for the genotype AA, AG, GG. There are 5 people with the AA genotype, 100 with the AG genotype and 900 with the GG genotype. I coded GG genotype as 1, AG as 2 and AA as 3 and the p-value for the