Displaying 20 results from an estimated 400 matches similar to: "genetics: backward haplotype transmission association algorithm"
2005 Apr 19
2
cross validation and parameter determination
Hi all,
In Tibshirani's PNAS paper about nearest shrunken
centroid analysis of microarrays (PNAS vol 99:6567),
they used cross validation to choose the amount of
shrinkage used in the model, and then test the
performance of the model with the cross-validated
shrinkage in separate independent testing set. If I
don't have the luxury of having independent testing
set, can I just use the
2005 Sep 19
5
FDR analyses: minimum number of features
Dear List,
We are planning a genotyping study to be analyzed using false discovery
rates (FDRs) (See Storey and Tibshirani PNAS 2003; 100:9440-5). I am
interested in learning if there is any consensus as to how many
features (ie. how many P values) need to be studied before reasonably
reliable FDRs can be derived. Does anyone know of a citation where
this is discussed?
Bill Dupont
William D.
2005 Jun 08
2
CRAN task view for genetics
Hello to everyone!
I have built CRAN task view for genetics. For now I have not submit it
to CRAN yet and it can be accessible from:
http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.html
http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.ctv
I have not submitted it to CRAN, since I would like first some opinion
about it. Genetics is really so broad field that I belive one person
2011 Jan 12
0
adonis, amova and haplotype frequency
Dear All,
I'd like to perform adonis (from the vegan package) rather than amova
(in ade4) on some haplotype data, as I have crossed factors. Is there a
simple way to tweak the source to allow weights (haplotype frequencies)
in a similar way to amova?
Best
Simon
2010 Nov 09
0
haplotype and epistasis analysis using 3 or more SNPs?
Dear Mme/Mr.
Hope you are doing well. I am doing some genetic analysis using The R software and I have difficulties to find how I can perform an Interaction/epistasis analysis using 3 or more SNPs (=markers) ? (In the instructive manual, there is only an interaction/epistasis analysis with 2 markers).
In addition can you please inform me how I can perform Haplotype analysis and if there is an
2016 Apr 26
0
Haplotype network appearance
Hi,
I'm doing haplotype networks with the package pegas and the script from
Jimmy O'Donell's blog. The networks which I obtain are a little ugly and
I'd like to change some aspects of their appearance, but I'm just starting
with R and I don't know how to do it. I have the following problems:
-Some nodes overlap. I increase the scale.ratio but then I get a tiny
legend. So
2006 May 28
1
cartograms in R?
Q: Has anyone implemented cartograms [**] in R? A search on the R
site turned up
https://stat.ethz.ch/pipermail/r-sig-geo/2005-December/000698.html
which led to
http://www.okada.jp.org/RWiki/index.php?cmd=read&page=Rmap%A4%F2%BB%
C8%A4%C3%A4%BF%C3%CF%BF%DE%C9%BD%BC%A8&word=Rmap#content_1_35
which has (one form of) a cartogram as a PNG, but which doesn't seem
to have code. (The
2003 Feb 14
1
programs for genetics - haplo.score for R
A non-text attachment was scrubbed...
Name: not available
Type: text/enriched
Size: 1819 bytes
Desc: not available
Url : https://stat.ethz.ch/pipermail/r-help/attachments/20030214/7f3adccd/attachment.bin
2008 Apr 01
0
PAMR package question: How to plot Estimated probabilities for the training data and test data
Hi,
I have tried some time trying to figure out how to use pamr to plot multiclass
Estimated probabilities for the training data and test data?
Specifically, how to recreate the PAMR publication on PNAS with
Tibshrani et al. The publication is as attached. The plot I want to
do is Figure 5.
I have downloaded the pamr package and the function which gives
similar plot is pamr.plotcvprob
2005 Sep 22
0
FW: FDR analyses: minimum number of features
Dear Dr. Graves
Many thanks for your response. FDRs and their associated q values do
differ from Type I error rates and P values (See Storey and Tibshirani
PNAS 2003;100:9440-5). It is an approach that is rapidly gaining
popularity in the analysis of genomic data where we have massive numbers
of covariates measured on a comparatively modest number of subjects. To
my mind it is a real advance
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
2006 Mar 24
1
cox model for haplotypes
Hi,
Anybody knows a function that can fit haplotype data to a Cox model.
I've been searching it in the web without succeed.
I use "haplo.stats" package, but unfortunatelly it's not possible to
analyse survival data, amb I right?.
Thanks in advance.
Isaac Subirana (isubirana@imim.es)
[[alternative HTML version deleted]]
2009 Jan 22
1
infer haplotypes phasing trios tdthap
Dear R mailing list,
I have a dataset with genotypes from trios and I would like to infer
haplotypes for each mother, father and child. The package that I could
find that can do this is tdthap.
But when the mother is homozygous (e.g., 2/2) the haplotype is called as
not possible to infer (0); I would prefer for it to call the genotype
(2). From what I understand it is doing what I would like
2008 Apr 02
0
Is there any package can be used to solve individual haplotyping problem?
Hi all,
I am working for reconstructing haplotype from individual's SNPs. But I have
met a problem that most of paper and software I found are focus on
reconstructing haplotype from population's SNPs, rather than individual's
SNPs. I wonder is there any R package can be used to solve such problem?
Thanks in advance for any information,
Gang Chen
[[alternative HTML version
2009 Aug 25
1
USB question
Am I right in thinking that WINE doesn't fully support USB access from a
Windows program?
I'm curious about support for satnav (PNA) devices by the proprietary
support programs they use for updating maps, etc. The AppDB shows that
TomTom Home doesn't currently work, but what about the support programs
for the raft of cheap WindowsMobile devices, e.g. the Binatone X.350 or
Mio PNAs. I
2007 Jul 24
0
New package: pomp, inference for partially-observed Markov processes
To: cran at r-project.org
Subject: New package: pomp, inference for partially-observed Markov processes
The new package 'pomp' is built around a very general realization of nonlinear
partially-observed Markov processes (AKA state-space models, nonlinear
stochastic dynamical systems). The user provides functions specifying the
model's process and measurement components. The
2007 Jul 24
0
New package: pomp, inference for partially-observed Markov processes
To: cran at r-project.org
Subject: New package: pomp, inference for partially-observed Markov processes
The new package 'pomp' is built around a very general realization of nonlinear
partially-observed Markov processes (AKA state-space models, nonlinear
stochastic dynamical systems). The user provides functions specifying the
model's process and measurement components. The
2015 Jul 24
0
Rcartogram package - error message
I am trying to install two R packages to produce cartograms like in the work
of Gastner and Newman:
http://www.pnas.org/content/101/20/7499.full.pdf
but I have a problem installing Rcartogram and rdyncall packages.
Both are not available in CRAN and have to be installed from archivea and
produce errors:
> install.packages("C:/Users/Milena/Downloads/*Rcartogram*_0.2-2.tar.gz",
>
2004 Dec 13
2
classification for huge datasets: SVM yields memory troubles
Hi
I have a matrix with 30 observations and roughly 30000 variables, each
obs belongs to one of two groups. With svm and slda I get into memory
troubles ('cannot allocate vector of size' roughly 2G). PCA LDA runs
fine. Are there any way to use the memory issue withe SVM's? Or can you
recommend any other classification method for such huge datasets?
P.S. I run suse 9.1 on a 2G RAM