Displaying 5 results from an estimated 5 matches for "microsatellit".
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microsatellite
2012 Sep 10
1
Calculating Linkage Disequilibrium for Microsatellite Markers?
Dear R helpers,
I am trying to test for linkage disequilibrium (LD) in R between all pairs
of loci. Importantly, my loci are microsatellites and have up to 30
alleles per locus. Do you know of any R packages that can either (1)
calculate measures of LD directly or (2) test for the presence of LD within
a statistical framework? Every package I have run across seems to be only
able to handle biallelic (e.g., SNP) data. I have
searche...
2010 Sep 01
2
Rd-file error: non-ASCII input and no declared encoding
...:
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 genetic data of Tetragonula bees}
\description{
Genetic data for 236 Tetragonula (Apidae) bees from Australia
and Southeast Asia, see Franck et al. (2004). The data give pairs of
alleles (codominant markers) for 13 microsatellite loci.
}
\usage{data(tetragonula)}
\format{
Two objects...
2008 Apr 19
1
resampling from distributions
...of shared 1) behaviours and 2)
alleles between numerous individuals. Pasted below ('propshared' function)
is what I have now and and works very well for calculating the proportion of
shared behaviours where the data is formatted with each column as a
behaviour and each row an individual. Microsatellite genotypes are
formatted differently. An example is below. Each row is an individual and
each column is one allele from a single locus. From the below values L1
and L1.1 each give a copy of an allele for same locus. Occasionally values
from different loci will have the same value altough these...
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?
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2010 Jul 18
6
CRAN (and crantastic) updates this week
...write both files and in-memory raw vectors.
* poistweedie (1.0)
David Pechel Cactcha
http://crantastic.org/packages/poistweedie
Simulation of models Poisson-Tweedie.
* polysat (0.1)
Lindsay V. Clark
http://crantastic.org/packages/polysat
polysat is a collection of tools to handle microsatellite data of any
ploidy (and samples of mixed ploidy) where allele copy number is not
known in partially heterozygous genotypes. It can import and export
data in ABI GeneMapper, Structure, ATetra, Tetrasat/Tetra, GenoDive,
SPAGeDi, and binary presence/absence formats. It can calculate
pairwi...