similar to: looking for a faster way to compare two columns of a matrix

I have a list (length 750), each element containing a vector of unique strings (unique gene ids), with length up to ~40 (median 15). I want to compile a matrix of all possible triplets and their frequency within gene elements. Using combn and a lot of looping, I am accomplishing this but it is VERY slow. I've tried to figure out a way to vectorize this, using "match" and

Hi List, I'm hoping to get opinions for enhancing the efficiency of the following code designed to take a vector of probabilities (outcomes) and calculate a union of the probability space. As part of the union calculation, combn() must be used, which returns a matrix, and the parallelized version of lapply() provided in the multicore package requires a list. I've found that

I'm working with genotype data in a frequency table: > a=matrix(1:16, nrow=4) > rownames(a)=c("AA","AT","TA","TT") > a [,1] [,2] [,3] [,4] AA 1 5 9 13 AT 2 6 10 14 TA 3 7 11 15 TT 4 8 12 16 'AT' and 'TA' are essentially the same, and I'd like to combine (add) the rows to reflect

While building a package, I see the following: * checking R code for possible problems ... NOTE cheat.fit: no visible binding for global variable 'Zobs' plot.jml: no visible binding for global variable 'Var1' I see the issue has come up before, but I'm having a hard time discerning how solutions applied elsewhere would apply here. The entire code for both functions is below,

Hi there! I can't find any information about creating combinations with repetitions in R. The function combn() does create combinations, but _without_ repetitions. Here is what I need to do: svIter <- 1000 xx <- matrix(rnorm(m*n), c(m, n)) sequence <- seq(range(xx)[1], range(xx)[2], length.out = svIter^(1/q)) expand.grid(secuence, secuence, .../q times/..., secuence) That is,

Hello all, I am brand new to R and doing an exercise for a class. I need to find the nearest neighbour for points in the following matrix: > DistanceMatrix x1 x2 x3 x4 x5 [1,] 0.000000 2.828427 1.581139 2.236068 2.000000 [2,] 2.828427 0.000000 1.581139 4.123106 2.000000 [3,] 1.581139 1.581139 0.000000 2.549510 2.121320 [4,] 2.236068 4.123106 2.549510

Hello! I have a regular data frame (DATA) with 10 people and 1 column ('variable'). Its cases are people with names ('a', 'b', 'c', 'd', 'e', 'f', etc.). I would like to write a function that would sum up the values on 'variable' of all possible combinations of people, i.e. 1. I would like to write a loop - in such a way that it

HI, You can also try this: d<-1:25 A<-sample(combn(20:30,2)) B<-sample(combn(20:30,2)) lapply(d,function(x) matrix(c(1,A[x],B[x],1),2,2)) [[1]] [,1] [,2] [1,] 1 23 [2,] 27 1 [[2]] [,1] [,2] [1,] 1 21 [2,] 21 1 [[3]] [,1] [,2] [1,] 1 29 [2,] 23 1 [[4]] [,1] [,2] [1,] 1 25 [2,] 20 1 [[5]] [,1] [,2] [1,] 1 23 [2,]

For a package application, I want to generate all 1-way, or 2-way, ... combinations of factors, symbolically, as a matrix. E.g., all two-way terms among 4 factors. > factors <- LETTERS[1:4] > combn(4,2) [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 2 2 3 [2,] 2 3 4 3 4 4 But I want to replace the numbers I in the above by factors[I]. I know I

Hello! I've a problem with the combn function and a set of vector. I would like to make a simple combination where, instead of scalars, i would like to combine vector, in order to form matrixes. In other words, i have nineteen 6-items vectors (for example coef1-coef19), that i would like to combine in n!/k!(n-k)! 6x6 matrixes. I tried with a code like this mma <-

Hi all, I would like to know how can I sort the cols of a matrix by the sum of their elements. a <- matrix(as.integer(rnorm(25,4,2)),10,5) colnames(a) = c("alfa","bravo","charlie","delta","echo") I guess I should use colSums, and then rearrange the matrix somehow according to the result. My idea is to display a "sorted" barplot:

I've created a .Rd file (below), then converted that to .sgml using R CMD Rdconv --type=Ssgm combn.Rd > combn.sgml The output (shown below) is missing some of the sections: arguments seealso examples If instead I convert to .d (below), the same sections are missing, and the "note" section is included but without the necessary newline.

Hi, I am currently attempting to write a small program for a randomization test (based on rank/combination) for matched pairs. If you will please allow me to introduce you to some background information regarding the test prior to my question at hand, or you may skip down to the bold portion for my issue. There are two sample sizes; the data, as I am sure you guessed, is matched into pairs and

Hi, i am working on a problem where i need to compute the products of all possible combinations of size m of the elements of a vector. I know that this can be achieved using the function combn(), e.g.: > vector <- 1:6 > combn(x = vector, m = 3, FUN = function(y) prod(y)) In my case the vector has 2000 elements and i need to compute the values specified above for m = 32. Using combn() i

Hi, anyone interested in this: I tried to simply this loop with lapply or something but haven't figured it out: mapt = c("203929_s_at", "203930_s_at", "203928_x_at", "206401_s_at") mapt.combn <- lapply(1:4, function(i) combn(mapt, i)) out = list() k = 1 for (i in 1:length(mapt.combn)){ for (j in 1:ncol(mapt.combn[[i]])){ out[[k]] =

Hi R-helpers, I've been struggling with a problem for most of the day (!) so am finally resorting to R-help. I would like to subset the columns of my dataframe based on the frequency with which the columns contain non-zero values. For example, let's say that I want to retain only those columns which contain non-zero values in at least 1% of their rows. In Excel I would calculate a row

Hi, I am trying to use a vector of indices to select some rows from a matrix. But before I can do that I somehow need to convert 'combinations' into a list, since 'mode(combinations)' says it's 'numerical'. Any idea how I can do that? library("combinat") combinations <- t(combn(8,2)) indices <- c(sample(1:length(combinations),10)) # convert ???

Dear R Group I have a matrix object in R, where i want to retain only those columns which have each row from a different group.. see the example below.. team1<-c("a1","a2","b1","b2","b3","c1","c2") teams<-combn(team1, 3) I want a function which will delete all columns in the teams matrix that have more than 1 row

Dear All, I have a dataframe made up of individual beetles consisting of individual number, family number, mother's family number, father's family number, and sex of the beetle. I would like to pair up the individuals for breeding. I would, however, like to avoid breeding beetles of the same sex (obviously), the same family, and with the same mother's family or father's family,

Dear developeRs, I encounter the following problem: in the current version of my package FrF2, certain calls to a functioni do not work when package combinat is loaded, because function combn from combinat masks the function from utils that my package uses. I tried to solve this issue by importing function combn into the namespace of FrF2; I don't need to export it, I just want to use it