search for: myseq

Hi Function sequence() repeatedly concatenates its output, and this is slow. It is possible to improve on the performance of sequence by defining myseq <- function(x){unlist(sapply(x,function(i){1:i}))} The following session compares the performance of myseq(), and sequence(), at least on my G5: > identical(sequence(1:50),myseq(1:50)) [1] TRUE > system.time(ignore <- sequence(1:800)) [1] 1.16 0.88 2.07 0.00 0.00 > system.time...

Hi Function sequence() repeatedly concatenates its output, and this is slow. It is possible to improve on the performance of sequence by defining myseq <- function(x){unlist(sapply(x,function(i){1:i}))} The following session compares the performance of myseq(), and sequence(), at least on my G5: > identical(sequence(1:50),myseq(1:50)) [1] TRUE > system.time(ignore <- sequence(1:800)) [1] 1.16 0.88 2.07 0.00 0.00 > system.time...

Hi, I have encountered this problem quite a few times and thought I would ask. Let's say that I have two endpoints, a and b, which are integers. If a <= b, I would like to get a:b, but if a > b, then numeric(0), for example: myseq(3,5) => 3:5 myseq(3,3) => 3 myseq(3,2) => numeric(0) The operator : just gives decreasing sequences in the latter case, and I could not coax seq into doing this either (of course the documentation is correct, it never claims that I could). Should I just write my own function, or is there...

...000000 b0002 0.035122 0.065854 b0003 0.024193 0.070968 b0004 -0.096729 0.084112 b0005 -0.973469 0.091837 b0006 -0.402713 0.108527 b0007 0.680672 0.123950 b0008 -0.209779 0.072555 b0009 -0.013334 0.046154 b0010 0.952128 0.143617 suppose you have these data into a data frame called myseqs [see the R documentation in how to upload these data, you can try > myseqs <- edit(read.table()) ] # you need to load the necessary libraries library(mva) # basic clustering library(cluster) # more clustering algorithms # then you need to calculate the 'distances' betw...

...class "factor" but class "numeric" was supplied # In addition: Warning message: # variable 'myfac' is not a factor in: model.frame.default(Terms, newdata, na.action = na.action, xlev = object$xlevels) # Isn't there an easier way than this? c1 <- coef(mymod1) myseq <- seq(0,1, length.out=10) newdf <- data.frame(1, myseq) linearPredictor <- as.matrix(newdf) %*% c1 p2 <- 1/ (1 + exp(-linearPredictor)) # But there is a big disaster if you just try the obvious thing # of plotting with # lines(myseq,p2) # The line does not show up where you hope in...

...em is that I would like to write in every cell the value of the corresponding entry of the original matrix, not is logarithm. Does anyone know how to get this done? Or the other way around: leave the data as is, but use a color log scale. Many thanks Lorenzo library(plotrix) set.seed(1234) myseq <- abs(rnorm(25)) myseq[20] <- 100 #introduce outlier! A <- matrix(myseq, ncol=5,nrow=5) #nasty looking figure pdf("test_color_scale.pdf") oldpar<-par( mar = c(4.5,5, 2, 1) + 0.1, cex.axis=1.4,cex.lab=1.6,cex.main=1.6) color2D.matplot(A,main="Title",c(0.2,1),c...

Hi, I am very new to R and wanted to know if there is a package that, given very long nucleotide sequences, searches and identifies short (7-10nt) motifs.. I would like to look for enrichment of certain motifs in genomic sequences. I tried using MEME (not an R package, I know), but the online version only allows sequences up to MAX 60000 nucleotides, and that's too short for my needs..

Hi. Suppose I have a vector that I partition into disjoint, contiguous subvectors. For example, let v = c(1,4,2,6,7,5), partition it into three subvectors, v1 = v[1:3], v2 = v[4], v3 = v[5:6]. I want to find the maximum element of each subvector. In this example, max(v1) is 4, max(v2) is 6, max(v3) is 7. If I knew that the successive subvector maxima would never decrease, as in the example,

Hi there, I am looking for R-packages that can help me visualize properties on nucleotide sequences. I want to display sequences in the 1-100K base range as lines and plot features above and below those lines. Any ideas would be welcome. Thanks, Bernd [[alternative HTML version deleted]]

Dear R users: > append(1:5, 0:1, after=2) [1] 1 2 0 1 3 4 5 If I want to repeat the appended value every 2 like the following: [1] 1 2 0 1 3 4 0 1 5 How should I modify? Thank you for any help.

I am a new R user. As a test, I want to write a simple code that does the following simulation: 1. Randomly generate a number from a distribution, say, Poisson. Let's say that number is 3. 2. Randomly generate 3 numbers from another distribution, say, Normal. 3. Compute the sum of the numbers generated in step 2 and read it into a vector, V. 4. Repeat steps 1 through 3 for 100,000 times. 5.

In my database the id for a field is 810. RoR thinks that it is 809. My log file (below) shows that just before the insert it grabs the next sequence value. I dont think it should do that. This causes problems further down the line when trying to access the Person object. Development Log file : "SQL (0.016000) select people_seq.nextval id from dual Person Create (0.015000) INSERT