similar to: Calculating Linkage Disequilibrium for Microsatellite Markers?

Displaying 20 results from an estimated 200 matches similar to: "Calculating Linkage Disequilibrium for Microsatellite Markers?"

2005 Aug 04
1
linkage disequilibrium
Dear all, I'm using the package "Genetics", and I'm interested in the computation of D' statistics for Linkage Disequilibrium, for which the LD() command has been realised. Unfortunately I don't find any reference on "how" the D' is computed by the LD() function. In the package documentation it is generally referred as "MLE" estimation, but
2006 May 30
1
sib TDT transmission/disequilibrium test
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
2010 Sep 01
2
Rd-file error: non-ASCII input and no declared encoding
Dear list, I came across the following error for three of my newly written Rd-files: non-ASCII input and no declared encoding I can't make sense of this. Below I copied in one of the three files. Can anybody please tell me what's wrong with it? Thank you, Christian \name{tetragonula} \alias{tetragonula} \alias{tetragonula.coord} \docType{data} % \non_function{} \title{Microsatellite
2007 Jun 25
2
Re : Half of a heatmap
> I am trying to produce a heatmap of pairwise correlations, but since the matrix is > symmetric, I only need either the upper or the lower triangle. I have scoured the > web and R documentation, but I have not been able to find a way to produce such a > figure. Is there a simple way to produce a heat map with only the part above or > below the diagonal? You might want to check
2008 Apr 19
1
resampling from distributions
Hello All, Once again thanks for all of the help to date. I am climbing my R learning curve. I've got a few more questions that I hope I can get some guidance on though. I am not sure whether the etiquette is to break up multiple questions or not but I'll keep them together here for now as it may help put the questions in context despite the fact that the post may get a little long.
2006 Apr 27
2
Incomplete Trio in TDT analysis
I am involved in a study where, as in most of life, men demonstrate themselves to be recalcitrant. So while we have many probands and most of their mothers we only have about 50% of the trios being complete. I have been running tdt and trio.types. It appears as if it is ignoring the duos. Sometimes a duo can be informative. For instance Father ..missing Mother 1/2 Proband 1/1 This duo shows that
2005 Mar 03
1
calculating of linkage-disequilibrium measures?
Hi , is it possible to calculate ld-measures D, D', r and perhaps corresponding p-values with r IF THE PHASE IS KNOWN? The genetics - package provides the LD function only for ambigious phase. Thank you very much Bettina Kulle
2010 Feb 28
1
Combining 2 columns into 1 column many times in a very large dataset
*Combining 2 columns into 1 column many times in a very large dataset* The clumsy solutions I am working on are not going to be very fast if I can get them to work and the true dataset is ~1500 X 45000 so they need to be efficient. I've searched the R help files and the archives for this list and have some possible workable solutions for 2) and 3) but not my question 1). However, I include
2009 Feb 09
0
Generating missingness on SNP data
Dear all, I generated a dataset with 500 unrelated individuals and 10 biallelic SNPs. From this dataset,I would like to create data with 5% missingness on genotype information at random and also data with 5% genotyping error. Can someone help me with how I can do it. [[alternative HTML version deleted]]
2012 Nov 13
2
Discrete trait Ornstein–Uhlenbeck in R?
Is there a package that will allow me to fit Brownian motion and Ornstein?Uhlenbeck models of evolution for discrete traits? I know that geiger and ouch have commands for fitting these models for continuous traits, but these aren't suitable for discrete trait evolution, correct? -- View this message in context:
2017 Jul 09
0
[R-pkgs] R package hypred: Simulation of genomic data in applied genetics
Dear Frank, I hope everything is well with you. ? ?First of all? ?, I? ?'d like thank you for your nice genomic simulation program (*hypred *package) and also for taking your time to answer my question. Dear Frank, I'm a PhD student of animal breeding science from Iran. Unfortunately although I try more time for running your package in order to simulate of a historical and reference
2008 May 05
1
genotypes simulation
Hello, I am having really hard time finding a good article about simulating genotypes of cases and controls at a disease locus using R. if you guys can point me or guide me where i can find more information, it will be helpful. thanks, Claire -- View this message in context: http://www.nabble.com/genotypes-simulation-tp17065607p17065607.html Sent from the R help mailing list archive at
2012 Mar 12
1
Speeding up lots of calls to GLM
Dear useRs, First off, sorry about the long post. Figured it's better to give context to get good answers (I hope!). Some time ago I wrote an R function that will get all pairwise interactions of variables in a data frame. This worked fine at the time, but now a colleague would like me to do this with a much larger dataset. They don't know how many variables they are going to have in the
2006 Jul 09
0
syntax: multiple markers at this line
I am using the following youtube method: def youtube.videos.list_by_tag and I get the syntax error: multiple markers at this line. any help please. -- Posted via http://www.ruby-forum.com/.
2008 Sep 29
0
Adding markers with info bubbles
Hi All, I am following an example of adding markers on a openlayers interface. Having difficulties when trying to add markers into a custom tiled map. Is there anyone that can help me? If you need more info, I can provide the code. Thanks, Gokalp Selcuk gselcuk at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL:
2017 Dec 13
0
running Cox regression model for 1000 markers
HI All, Sorry to bother you. I have a data matrix with 1000 genes in rows and 100 samples in columns; I need to run Cox regression model for each of the 1000 markers. I know how to run Cox regression model for individual marker. Does anyone know a R package or method to run Cox model for those 1000 markers and then output results in a data frame? Thank you, Ding
2009 Dec 18
1
[PATCH] nouveau: don't emit reloc markers for bo's that are mapped
Signed-off-by: Maarten Maathuis <madman2003 at gmail.com> --- src/gallium/drivers/nouveau/nouveau_stateobj.h | 9 +++++++++ 1 files changed, 9 insertions(+), 0 deletions(-) diff --git a/src/gallium/drivers/nouveau/nouveau_stateobj.h b/src/gallium/drivers/nouveau/nouveau_stateobj.h index 9aee9e4..6c40f64 100644 --- a/src/gallium/drivers/nouveau/nouveau_stateobj.h +++
2010 Jul 28
1
Track Markers?
Hello. I have tried filing this as a support request, but have not received any reply in 3 weeks now so am trying this route instead. I hope this is okay. We are trying to talk a record label into offering FLAC streams for a band, and they have finally agreed to do this. Trouble is, the albums have segues - no silences between tracks - and the label want to only offer whole albums. Therefore -
2009 Mar 29
1
Darker markers for symbols in lattice
In lattice, using the command trellis.par.get for superpose.symbol, plot, symbol and/or dot.symbol shows that we can specify alpha, cex, col, fill (for superpose.symbol and plot.symbol), font, and pch. Trial and error shows that the font affects letters but not pch=1 or pch=3 (open circles and plus signs.) I want to use open circles and plus signs, keep the colors and cex I've specified but
2018 May 12
2
[bug] --keep-foreign-metadata discards WAV cue markers
Hello, I noticed that option --keep-foreign-metadata discards WAV cue markers. Here is how to reproduce the bug: 1) Create a 24-bit 96khz in SoundForge8, add 20 seconds of silence, and add two markers with "m" key shortcut 2) Save it, compress it with "flac --keep-foreign-metadata testmarkers.wav" 3) Decompress it with "flac -d testmarkers.flac" 4) Open the