Displaying 20 results from an estimated 1000 matches similar to: "R, joint scaling test, quantitative genetic analysis & sensitivity to model violations"
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
2010 Oct 04
0
glmer or not - glmer model specification
Hello,
I'm having some trouble figuring out the correct model specification for
my data. The system consists of multiple populations of an organism,
which have been genetically sampled for several years. The problem is
this: A minority of individuals are found in more than one sample,
either they have survived into the next sampling at the same location,
or have migrated to another another
2008 Jan 21
2
reordering huge data file
Dear R-experts,
My problem is how to handle a 10GB data file containing genotype data. The file is in a particular format (Illumina final report) and needs to be altered and merged with phenotype data for further analysis.
PERL seems to be an frequently used solution for this type of work, however I am inclined to think it should be doable with R.
How do I open a text-file, line by line,
2011 Jan 03
0
Using PCA to correct p-values from snpMatrix
Hi R-help folks,
I have been doing some single SNP association work using snpMatrix. This works
well, but produces a lot of false positives, because of population structure in
my data. I would like to correct the p-values (which snpMatrix gives me) for
population structure, possibly using principle component analysis (PCA).
My data is complicated, so here's a simple example of what
2002 Nov 27
0
R genetics package now available
The "genetics" package for handling single-locus genetic data is now
available on CRAN in both source and Windows binary formats. The purpose of
this package is to make it easy to create and manipulate genetic
information, and to facility use of this information in statistical models.
The library includes classes and methods for creating, representing, and
manipulating genotypes
2002 Nov 27
0
R genetics package now available
The "genetics" package for handling single-locus genetic data is now
available on CRAN in both source and Windows binary formats. The purpose of
this package is to make it easy to create and manipulate genetic
information, and to facility use of this information in statistical models.
The library includes classes and methods for creating, representing, and
manipulating genotypes
2010 Aug 23
3
DNA sequence Fst
Hi,
I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst,
Heterozygosity and such summary statistics. Package Adagenet converts the
DNA sequence into retaining only retaining the polymorphic sites and then
calcuates Fst.. but is there any other way to do this? I mean analyse the
DNA sequence as it is.. and calculate the statistics?
Thanks!
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2007 Jan 21
2
efficient code. how to reduce running time?
Hi,
I am new to R.
and even though I've made my code to run and do what it needs to .
It is taking forever and I can't use it like this.
I was wondering if you could help me find ways to fix the code to run
faster.
Here are my codes..
the data set is a bunch of 0s and 1s in a data.frame.
What I am doing is this.
I pick a column and make up a new column Y with values associated with that
2007 Nov 29
1
configure the margin of the plot
I'm trying to put two plots side-by-side in two panels. Since the
y-axis of the two plots is the same, I want to leave out the y-axis of
the second plot.
And the two plots look quite separate from each other. Is there any way
to have them stay closer to each other? I've tried to adjust mar option
of par but it has a global effect as I see the left margin of the first
plot will be
2009 May 11
0
Tasks
Hi folks
I have some tasks for you on the Xen packages:
* copyright file
I doubt that this is in any way current.
* pvgrub
This contains several parts which needs to be statically linked
together:
- minios, libxenctrl, libxenguest, libxenstore, all built out of the
xen tree,
- patched grub,
- patched newlib and
- a libz.
- ioemu/dom0 userspace
The upstream build uses a clone
2013 Jun 27
0
Bug report on xen-utils-4.1: qemu-dm crashes with exit status 1
On Wed, Jun 26, 2013 at 01:48:03PM -0400, Alexandre Rebert wrote:
> We found a crash in qemu-dm contained in the xen-utils-4.1 package. You are being
> contacted because your are listed as one of the maintainer of xen-utils-4.1.
xen-utils-4.1 is not in unstable, so this is not really helpful.
> The bug report that will be submitted to the bug tracker is available at the
> following
2007 Jun 19
1
genetics package not working
Has something changed in R that requires an update in the genetics package
by Gregory Warnes? I am using R version 2.5.0
This used to work
> summary(founders[,59])
to prove that it is a genotype class
> class(founders[,59])
[1] "genotype" "factor"
Now when I issue the command:
> summary(founders[,59])
I get:
Error in attr(retval, "which") <- which :
2009 Jan 19
1
Deleting columns where the frequency of values are too disparate
Hello R-help community,
I have another question about filtering datasets.
Please consider the following "toy" data matrix example, called "x" for simplicity. There are 20 different individuals ("ID"), with information about the alleles (A,T, G, C) at six different loci ("Locus1" - "Locus6") for each of these 20 individuals. At any single locus
2007 Mar 16
1
ideas to speed up code: converting a matrix of integers to a matrix of normally distributed values
Hi all,
[this is a bit hard to describe, so if my initial description is
confusing, please try running my code below]
#WHAT I'M TRYING TO DO
I'd appreciate any help in trying to speed up some code. I've written
a script that converts a matrix of integers (usually between 1-10,000
- these represent allele names) into two new matrices of normally
distributed values (representing
2012 Jun 14
1
Can someone recommend a package for SNP cluster analysis of Fluidigm microarrays?
I know that there are quite a few packages out that there for cluster
analysis. The problem that I am facing is finding a package that will not
incorporate all my samples into clusters but just the samples that fit a
threshold (that I have not set yet and may need help finding the right
level) for genotyping. It should be able to "no call" samples outside the
clusters. It also needs to
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 May 03
1
Vector searching and counting speed optimization
R-users,
I'm seeking any suggestions on optimizing some code for speed. Here's
the setup: the code below is part of a larger chunk that is calculating
Fst values across loci and alleles. This chunk is designed to calculate
the proportion ('p.a') of an allele ('a') at a locus in each population
('p') and the proportion of individuals heterozygous for that
2006 May 07
0
How to a handle an error in a loop [Broadcast]
This ought to work:
resultdt <- lapply(PGWide[, 240:389], function(x, ...) try(tdt(x, ...)))
You can then check the class of each component to see which one failed.
Andy
From: Farrel Buchinsky
>
> "Berton Gunter" <gunter.berton at gene.com> wrote in message
> news:008601c67097$de1b46e0$5bc4fea9 at gne.windows.gene.com...
> > ?try
> >
> > as in
2011 Jun 27
1
Hardy Weinberg Simulation
Hello,
I am trying to simulate 10 relicates of 100-tables. Each table is a 2 x 3
and 80% pf the tables are true nulls and 20% are non-nulls. The nulls follow
the Hardy Weinberg distribution (ratio) 1:2:1.
I have the code below but the p-values are not what I am expecting. I want
to use the Cochran Armitage trend test to get the p-values.
num.reps=10
num.vars=1000
pi0 = 80
num.subjects = 100
2006 Apr 06
4
Reshaping genetic data from long to wide
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