similar to: how to group a large list of strings into categories based on string similarity?

Dear folks, Please welcome a newbie both to R and the mailing list :). I am currently working on a sequencing project, and heard about R as well as some of its packages for next gen sequencing, and decided to give it a try. Starting with ShortRead, I found a document (http://www.bioconductor.org/packages/2.5/bioc/vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf) which does mention

Hi, I understand ShortRead::FastqStreamer will read chunks in parallel depending on the value of ShortRead:::.set_omp_threads I see this discussed here: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004355.html and nowhere else. It probably should be documented in ShortRead. Possibly this has already changed for I am using still R 3.1.0. I thought I'd check. Oh, and, in my

Dear R-Help, I would be most grateful if you could inspect the attached install file. I would like to be able to use ShortRead to generate QA reports for Genome Analyzer output data. OS: Linux CentOS 5.3 on HP Proliant server . In process of installing "R" package after configuration flagging some missing modules-libraries the install process will not perform 'make' function.

Hello everyone. There is a new competition, outlined on the blog dataists<http://www.dataists.com/2010/10/using-data-tools-to-find-data-tools-the-yo-dawg-of-data-hacking/>, inviting us to analyse statistics of the use of R packages (collected from 52 R users), to create a R-package suggestion engine for ourselves. Since I noticed several bloggers already wrote about it (as I have detailed

Hello all, I upgraded my R workstation, and to my dismay, only one core appears to be used during intensive computation of a bioconductor function. What I have now is two dual-core Xeon 5160 CPUs and 10 GB RAM. When I fully load it, top reports about 25% user, 75% idle and 0.98 short-term load. The archives gave nothing helpful besides mention of snow. I thought of posting to HPC, but this system

I have a two part question Part 1) I am trying to remove characters in a string based on the position of a key character in another string.? I have a solution that works but it requires a for-loop.? A vectorized way of doing this has alluded me.? CleanRead<-function(x,y) { ? if (!is.character(x)) ??? x <- as.character(x) ? if (!is.character(y)) ??? y <- as.character(y) ?

Based on some testing it seems to me that if I have a package with a dataset in /data a Sweave vignette in inst/doc (but no associated pdf file) the vignette loads the data in /data through data(dataset) and I do a R CMD build R will try to build the pdf version of the vignette, but will be unable to find the dataset in data because the package is not yet installed. However, if I do

In pvec(list(1, 2), FUN, mc.cores=2) FUN sees integer() arguments whereas pvec(list(1, 2, 3), FUN, mc.cores=2) FUN sees list() arguments; the latter seems consistent with pvec's description. This came up in a complicated Bioconductor thread about generics and parallel evaluation https://stat.ethz.ch/pipermail/bioc-devel/2012-October/003745.html One relevant point is that a

Hi, I have two global raster maps, each of the same variable but from different sources. The values range from 0 to 5 in whole numbers. Is there a statistical test in R that can quantify the similarity of the spatial patterns (i.e., highs and lows)? Thanks, -- View this message in context: http://r.789695.n4.nabble.com/map-similarity-spatial-autocorrelation-in-R-tp4647877.html Sent from the

Hello. I'm looking for a fast way to group by similarity many (5-10k) long (2-10k points) time series. Using PAM on distance matrix obtained via as.dist(1-abs(cor(data))) produces usable results but it's rather slow and doesn't catch slightly shifted time series. DTW implementation from package 'dtw' is orders of magnitude slower even with global window constraints which

I have been reading a paper whereby the authors took values from Sorensons dissimilarity index and values from a percentage similarity index and applies G-Testing to the table of values. This is carried out to assess the differences in spider faunas (Strattton and Uetz, 1979). I like the method but have been trying to work out what function in R to use to get the percentage similarity. I have

Hi, I would like to know the similarity between variables, but I don't exactly how begin and as from what dataframe or matrix! I have a matrix where in row I have 'Good', 'Medium','Bad' and in columns I have my Criterions ! What function and package should I use? Thanks a lot Sabine --------------------------------- ils, photos et vidéos ! [[alternative

Dear all, I am using a program that generates similarity matrices in the following non-redundant pairwise format. a b 0.4 a c 0.5 a d 0.3 b c 0.9 b d 0.6 c d 0.2 matrix(c('a','a','a','b','b','c','b','c','d','c','d','d',.4,.5,.3,.9,.6,.2),byrow=F,nrow=6) I would like to convert this to a

I'm interested in clustering my data using the Gower Similarity Coefficient, and I was wondering if R is capable of using that metric Timothy Rye [[alternative HTML version deleted]]

>x=c(3.05176E-05,0.000457764,0.003204346,0.0138855,0.04165649,0.09164429,0.1527405,0.1963806,0.1963806,0.1527405,0.09164429,0.04165649,0.0138855,0.003204346,0.000457764,3.05176E-05) >y=c(0.0000306,0.0004566,0.0031985,0.0139083,0.0415539,0.0917678,0.1528134,0.1962831,0.1962994,0.1527996,0.0917336,0.0415497,0.0139308,0.0031917,0.0004529,0.0000301) I tried chisq.test, t-test, prop.test, etc,

Hello, It's just a strange coincidence that someone posted just very recently a question about matching. I know there are several match function in the base package (such as match, pmatch, charmatch, and the gsub etc) but I can't seem to use them wisely to be able to get what I need. suppose I have the following strings: "tets" "estt" "rtes7"

I am doing hierarchical clustering with cluster package.  I couldnot find similarity measures like matching coefficient, Jaccard coefficient and sokal and sneath. Could anyone please tell package with similarity measures for binary data? kind regards, Ms.Karunambigai M PhD Scholar Dept. of Biostatistics NIMHANS Bangalore India From cricket scores to your friends. Try the Yahoo! India

hi all, I am doing hierarchical clustering using similarity measures for binary data using package ade4 and hclust function. For method=8 and method = 9 of dist.binary, I am getting Na values. Hence, hclust function is giving error as Error in hclust(d8, method = "ward") :   NA/NaN/Inf in foreign function call (arg 11). I think the fact that due to zero in the denominator of the

Hello R-users, I've got a file with individuals as colums and the clusters where they occur in as rows. And I wanted a similarity matrix which tells me how many times each individual occurs with another. My eventual goal is to make Venn-diagrams from the occurence of my individuals. So I've this: cluster ind1 ind2 ind3 etc. 1 0 1 2 2 3 0 1 3

Dear All, I need to estimate the level of similarity of two strings. For example: string1 <- c("depending","audience","research", "school"); string2 <- c("audience","push","drama","button","depending"); The words in string may occur in different order though. What function would you recommend to use