similar to: Re: R-help Digest, Vol 9, Issue 11

A bit late, but you might like to look at http://www.qimr.edu.au/davidD/polyr.R Regarding the original posters queries: You can analyse polychoric correlations as if they were Pearson correlations using standard software (eg sem), and this usually doesn't do too badly, or go to AWLS (Browne) in LISREL etc, or ML analysis of the full multidimensional contingency table using programs such as

Ron Crump wrote: > Hi, > > I have a dataframe that contains pedigree information; > that is individual, sire and dam identities as separate > columns. It also has date of birth. > > These identifiers are not numeric, or not sequential. > > Obviously, an identifier can appear in one or two columns, > depending on whether it was a parent or not. These should > be

This is a bit late, but: > About two years ago there was a thread about this which suggested that at > that time nobody had these coefficients ready to go. > (a) has anyone in the meanwhile programmed them? http://www.qimr.edu.au/davidD/R/polyr.R > (d) I appreciate this last item is not strictly an R question, but my > intention is to use these as input into the sem package for

I don't know of any R package that can match all the functionality of LEM eg fitting equality constraints to model parameters a la LISREL. WRT dumping tables, I would have thought that as.data.frame.table does pretty much what you want, [not tested] newtab <- as.data.frame(table(a,b,c)) cat("dim\n") for(i in seq(1, ncol(newtab)-1) { cat(nlevels(newtab[,1]," ") }

Hi. I just noticed the paper by Morales and Nocedal Remark on "Algorithm 778: L-BFGS-B: Fortran Subroutines for Large-Scale Bound Constrained Optimization". TOMS 2011; 38(1): 7 http://www.ece.northwestern.edu/~morales/PSfiles/acm-remark.pdf which describes a couple of improvements (speed and accuracy) to the original Netlib code which AFAICT is that still used by optim() via f2c.

> Date: Mon, 20 Feb 2006 16:43:55 -0600 > From: Aldi Kraja <aldi at wustl.edu> > > Hi, > Using package gclus in R, I have created some graphs that show the > trends within subgroups of data and correlations among 9 variables (v1-v9). > Being interested for more details on these data I have produced also the > var-covar matrices. > Question: From a pair of two

Hi. I don't know if this a bug or just annoying to me: > x <- c(1,2,3,NA) > table(x, exclude=NULL) x 1 2 3 <NA> 1 1 1 1 > table(factor(x), exclude=NULL) 1 2 3 1 1 1 I don't think many people use factor(x, exclude=NULL): it is not the default handling of character data by read.table(). Cheers, David Duffy. -- | David Duffy (MBBS PhD)

On Fri, 16 Jan 2009, r-help-request at r-project.org wrote: > Date: Thu, 15 Jan 2009 13:29:03 +0100 > From: Pablo G Goicoechea <pgoikoetxea at neiker.net> > Subject: Re: [R] How to create a chromosome location map by locus ID > To: Sake <tlep.nav.ekas at hccnet.nl> > Cc: r-help at r-project.org > Message-ID: <496F2C0F.3040304 at neiker.net> > Content-Type:

On Mon, 8 Nov 2004 ssim at lic.co.nz wrote: > > Is there an add-on package in R for QTL interval mapping for outbred > population, eg. Haley-Knott regression method ? > > Stella I believe Karl Broman's R/QTL (http://biosun01.biostat.jhsph.edu/~kbroman/software/) and Brian Yandell's bim (http://www.stat.wisc.edu/~yandell/qtl/software/), Richard Mott's happyR

I couldn't resist adding a more literal answer unback <- function(x) { chars <- unlist(strsplit(deparse(x),"")) chars <- chars[-c(1,length(chars))] paste(gsub("\\\\","/",chars),collapse="") } unback("\n") | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph:

I couldn't resist adding a more literal answer unback <- function(x) { chars <- unlist(strsplit(deparse(x),"")) chars <- chars[-c(1,length(chars))] paste(gsub("\\\\","/",chars),collapse="") } unback("\n") | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph:

C?dric Finet wrote: > > I thank you for your answer but I do not understand yet why the Fisher?s exact > test does not work. And why is a "negative key". > > C?dric Finet > Running the original TOMS643 fortran code (R uses an f2c translation of this) says: FEXACT ERROR: 30 Stack length exceeded in f3xact. This problem should not occur. The integer hash key is

I have encountered the same problem with sshd -i (under Mandrake linux 6.1) as that described by Ben L Perkins, this time with 2.1.1p4: ... Last login: Mon Jul 17 12:04:50 2000 from orpheus.qimr.edu.au -bash: ?oe90: command not found -bash: glorious: command not found -bash: ?]r90: command not found -bash: marshall4: command not found Connection to orpheus.qimr.edu.au closed. log: Jul 17

Newsgroup members, I appreciate the help on this topic. David Duffy provided a solution (below) that was quite helpful, and came close to what I needed. It did a great job creating two vectors of dichotomous variables with a known correlation (what I referred to as a phi-coefficient). My situation is a bit more complicated and I'm not sure it is easily solved. The problem is that I must

Does anyone know if the sib TDT has been implemented in R 1. Spielman, R.S., and Ewens, W.J. (1998) A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test. Am J Hum Genet 62, 450-458 -- Farrel Buchinsky, MD Pediatric Otolaryngologist Allegheny General Hospital Pittsburgh, PA

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 there, If I do an lm, I get p-vlues as p-value: < 2.2e-16 Suppose am interested in exact value such as p-value = 1.6e-16 (note = and not <) How do I go about it? stephen

Hi R-users, I need to run Filliben correlation test, but I'm not able to find this function in any package. Perhaps it isn't in a package, but sometimes anybody have program this function or create a routine to estimate it. I found it in google and I hope what I found it's in this page, http://genepi.qimr.edu.au/staff/davidD/R/filliben.R but i can't open it. Anybody can help me?

If I run an analysis which generates statistical tests on many SNPs I would naturally want to get more details on the most significant SNPs. Directly from within R one can get the information by loading RSNPer (from Bioconductor) and simply issuing a command SNPinfo(2073285). Unfortunately, the command cannot handle a vector and therefore only wants to do one at a time. I tried the lapply and

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