Description Usage Arguments Value Author(s) References See Also Examples
Random samples are drawn from populations specified in tab.pop
. Pairwise relatedness is calculated by either "Bxy", "Sxy", "Mxy", "Li", "lxy", "rxy", "loiselle", "wang.fin", "wang",
"ritland", "morans.fin" or "morans" allele.sharing. Pairwise relatedness is calculated for different number of loci beginning with only one up to the maximum number of loci in the dataset. Reference populations can be set for the calculations if ref.pop="NA"
. tab.pop
is used as an estimate of overall allele frequencies. Distance between pairwise relatedness estimates are calculated using dist()
with euclidean calculation.
Graphically, a .pdf file is exported and the object Random.loci.differences
contains each pairwise difference for usage in further statistics.
1 2 3 4 |
tab.pop |
Specific dataframe of type inputformat. All populations which should be analyzed. |
ref.pop |
Specific dataframe of type inputformat. Population information which should be used as a reference for either threshold or allele frequency calculation. |
object |
logical - is tab.pop object. |
value |
String defining method to calculate allele sharing or similarity estimates. Can be set as "Bxy", "Sxy", "Mxy", "Li", "lxy", "rxy", "loiselle", "wang.fin", "wang", "ritland", "morans.fin" or "morans". |
bt |
Number of bootstrap replicates. |
file.output |
logical - should a .pdf file be sent as standard output in your working directory. |
Loci.test.Sys.Date().pdf |
Plot of linear regression of used loci and calculated mean estimate of relatedness from each bootstrapped replicate defined by |
Random.loci.differences |
List of differences in relatedness derived from bootstrap replicates. The x'th list element contains a matrix of means from replicates each over x random loci. |
Philipp Kraemer, <philipp.kraemer@uni-oldenburg.de>
Armstrong, W. (2012) fts: R interface to tslib (a time series library in c++). by R package version
0.7.7.
Blouin, M., Parsons, M., Lacaille, V. and Lotz, S. (1996) Use of microsatellite loci to classify indi-
viduals by relatedness. Molecular Ecology, 5, 393-401.
Hardy, O.J. and Vekemans, X. (1999) Isolation by distance in a contiuous population: reconciliation
between spatial autocorrelation analysis and population genetics models. Heredity, 83, 145-154.
Li, C.C., Weeks, D.E. and Chakravarti, A. (1993) Similarity of DNA fingerprints due to chance and
relatedness. Human Heredity, 43, 45-52.
Li, C.C. and Horvitz, D.G. (1953) Some methods of estimating the inbreeding coefficient. Ameri-
can Journal of Human Genetics, 5, 107-17.
Loiselle, B.A., Sork, V.L., Nason, J. and Graham, C. (1995) Spatial genetic structure of a tropical
understory shrub, Psychotria officinalis (Rubiaceae). American Journal of Botany, 82, 1420-1425.
Lynch, M. (1988) Estimation of relatedness by DNA fingerprinting. Molecular Biology and Evolu-
tion, 5(5), 584-599.
Lynch, M. and Ritland, K. (1999) Estimation of pairwise relatedness with molecular markers. Ge-
netics, 152, 1753-1766.
Oliehoek, P. A. et al. (2006) Estimating relatedness between individuals in general populations with
a focus on their use in conservation programs. Genetics, 173, 483-496.
Queller, D.C. and Goodnight, K.F. (1989) Estimating relatedness using genetic markers. Evolution,
43, 258-275.
Ritland, K. (1999) Estimators for pairwise relatedness and individual inbreeding coefficients. Ge-
netics Research, 67, 175-185.
Wang, J. (2002) An estimator for pairwise relatedness using molecular markers. Genetics, 160,
1203-1215.
1 2 3 4 5 6 7 8 9 10 | ## Loci.test to analyse Loci distribution in example data
data(demerelpop)
demerelpop.sp <- split(demerelpop,demerelpop[,2])
Loci.results <- Loci.test(demerelpop.sp[[1]][,1:8],
ref.pop = "NA", object = TRUE,
value = "rxy", bt = 10)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.