similar to: R package for computing state path using Viterbi algorithm

Hi all, I am using a discrete Hidden Markov Model with discrete observations in order to detect a sequence of integers. I am using the "hmm.discnp" package. I am using the following code: signature <- c(-89, -98, -90, -84, -77, -75, -64, -60, -58, -55, -56, -57, -57, -63, -77, -81, -82, -91, -85, -89, -93) quant <- length(-110:-6) # Initialize and train the hmm with the

(I think) I'd like to use the hmm.discnp package for a simple discrete, two-state HMM, but my training data is irregularly shaped (i.e. the observation chains are of varying length). Additionally, I do not see how to label the state of the observations given to the hmm() function. Ultimately, I'd like to 1) train the hmm on labeled data, 2) use viterbi() to calculate optimal labeling of

Dear list, Given a vector of logical values, say >a <- c(TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE) Are there any R functions that can tell whether there are two or more "TRUE" in a row in this vector? Thanks, Wuming

Dear list, When compiling the R-2.3.0 on FC4 x86_64, I got the following errors: make[3]: Entering directory `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main' gcc -Wl,--export-dynamic -L/usr/local/lib64 -o R.bin Rmain.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o

Hi: I use lm (linear model) to analyze 47 variables , 8 responses So I use loop to finish it . I want the program to show the results that P-value is less than 0.05. How can I cite the P-valus from lm result ? Ping The code: #using LM to model general fati for (j in 48:52) { for (i in 3:46){ gen.fat<-y_x[,j] gen.fat<-as.numeric(gen.fat) snp_marker<-y_x[,i] x<-colnames(y_x)

Dear list, In some places (for example, http://en.wikipedia.org/wiki/Support_vector_machine) , the polynomail kernel in SVM is written as (u'*v + 1)^d, while in the document of svm() in e1071 package, the polynomial kernel is written as (gamma*u'*v + coef0)^d. I am a little confused here: When doing parameter optimization (grid search or so) for polynomial kernel, does it need to tune

Dear list, I installed odesolve package (0.5-15) in R 2.3.1 in a Solaris server (Generic_118558-11 sun4u sparc SUNW,Sun-Blade-1000). The installing progress completed without errors, though several warnings like "Warning: Option -fPIC passed to ld, if ld is invoked, ignored otherwise" were outputed. However, when loading the odesolve package by library(odesolve), following error

Dear list, I have a problem on calculating the standard error of Goodman-Kurskal's gamma using delta method. I exactly follow the method and forumla described in Problem 3.27 of Alan Agresti's Categorical Data Analysis (2nd edition). The data I used is also from the job satisfaction vs. income example from that book. job <- matrix(c(1, 3, 10, 6, 2, 3, 10, 7, 1, 6, 14, 12, 0, 1, 9,

R Community - I am attempting to fit a model as described in Hampton, Bossaerts, and O'doherty (J. Neuroscience) 2006. They use a bayesian hidden markov model to model the Reversal Learning data. I have tried using HMM and depmixS4 with no success. My data is a Reversal Learning Task in which there are 3 sets of patterns over 3 blocks. The participant receives incorrect or correct

Dear all: I have a character object x with ' (single-quote) character. x <- c('"hydrolase activity","actin binding","3',5'-cyclic-nucleotide phosphodiesterase activity") I want to write a function that will identify ' and replaces with \' myf <- function(term){ if (grep("'",term)) {

Dear R users, I am looking for the source code of the implementation of ppr (Projection Pursuit Regression) in R. It will be great if citations of the source papers on which the implementation is based, are also provided. Thank you, Arvind Iyer, Grad student, Deptt. of Biomedical Engineering Viterbi School of Engineering University of Southern California, Los Angeles [[alternative HTML

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

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..

All Is there a package or library that will, given a nucleotide sequence 1. calculate the extinction coefficient at 260 nm for (Beer-Lambert's law) 2. calculate molecular weight 3. return it's complementary sequence I was able to find several packages that can do similar calculations for an amino acid sequence for proteins but none for nucleic acids. Any pointers, etc. would be

Hello, I'm struggling with understanding the output on the ancestral.pars() command from the phangorn package, I'm new to doing phylogenetic analyses using R. I used it on nucleotide data, and it works fine, I'm just not sure how to read the output. The output is phyDat class, and outputs a matrix for each node/leaf in the tree. I figured out that the matrix columns represent the four

I have following codes for ggplots. The legends are given in the plot do not match with the values specified in the codes given below. Your helps highly appreciated. Greg library(ggplot2) p <- ggplot(a,aes(x=NO_BMI_FI_beta ,y=FI_beta ,color= Super.Pathway))+ theme_bw() +theme(panel.border=element_blank()) + geom_point(size=3) p2<-p+scale_color_manual(name="Super.Pathway",

Hi folks, I'm pleased to introduce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export,

Hi folks, I'm pleased to introduce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export,

Hello all, thanks for your time and help. Below are my commands, and it generates a really nice plot, however I am not happy with the reorder() function. I would like the order to be the same as they appear in the genotype variable "genotype <- c("CJ1450 NW 4/25/12","CJ1450 BAL 4/25/12","CJ1450 NW 4/27/12","CJ1450 BAL 4/27/12","CJ1721 NW

library(sos) (mp <- findFn('{molecular properties}')) ????? ** found 7 matches in 4 packages and opened two web pages in my default browser with (a) the 7 matches and (b) the 4 packages. The first function was something for amino acids, like you suggested.? Two others returned compound and substance information from PubChem. ????? Does this help? ????? Spencer On