| Type: | Package |
| Title: | Accompaniment to Population Genetics with R: An Introduction for Life Scientists |
| Version: | 0.2 |
| Author: | Aki Jarl Laruson; Floyd Reed |
| Maintainer: | Aki Jarl Laruson <akijarl@gmail.com> |
| Description: | Provides several data sets and functions to accompany the book "Population Genetics with R: An Introduction for Life Scientists" (2021, ISBN:9780198829546). |
| License: | CC0 |
| Encoding: | UTF-8 |
| LazyData: | true |
| NeedsCompilation: | no |
| Packaged: | 2021-02-24 23:09:15 UTC; root |
| Depends: | R (≥ 3.5.0) |
| URL: | https://global.oup.com/academic/product/population-genetics-with-r-9780198829546?cc=gb&lang=en# |
| Repository: | CRAN |
| Date/Publication: | 2021-02-25 13:50:02 UTC |
Calculate and visualize LD
Description
Calculates the degree of linkage disequilibirum between two biallelic diploid loci and plots the results.
Usage
Dcalc(AABB, AaBB, aaBB, AABb, AaBb, aaBb, AAbb, Aabb, aabb)
Arguments
AABB |
Count of A and B double homozygotes. |
AaBB |
Count of A heterozygotes, B homozygotes. |
aaBB |
Count of a and B double homozygotes. |
AABb |
Count of A homozygotes, B heterozygotes. |
AaBb |
Count of double heterozygotes. |
aaBb |
Count of a homozygotes, B heterozygote. |
AAbb |
Count of A and b double homozygotes. |
Aabb |
Count of A heterozygotes, b homozygotes. |
aabb |
Count of a and b double homozygotes. |
Examples
#assign genotype counts
AABB=2
AaBB=0
aaBB=0
AABb=0
AaBb=1
aaBb=0
AAbb=1
Aabb=0
aabb=0
#run function
Dcalc(AABB, AaBB, aaBB, AABb, AaBb, aaBb, AAbb, Aabb, aabb)
Simulate and visualize a coalescent process
Description
A function that provides a simple starting off point to simulate a coalescent process.
Usage
coal(length, number, muscale, reps, prnt)
Arguments
length |
Length of sequence to simulate. |
number |
Number of starting lineages. |
muscale |
Mutation rate, scaled by 4Neu. |
reps |
Number of replicates to run. |
prnt |
Whether to print calculation output to the terminal (prnt=1), or not (prnt=0). |
Examples
#assign genotype counts
length=250
number=8
muscale=6.25 # theta = 4Neu = 25, theta/4 = 6.25
reps=100
prnt=0
#run function
coal(length, number, muscale, reps, prnt)
Drosphila melanogaster bw75 data
Description
A matrix of observed allele counts from Buri (1956). Each row contains observations starting at generation 1 in the first row, across 107 replicates of the number of bw75 allele.
Usage
fly
Source
Buri, P. (1956). Gene frequency in small populations of mutant Drosophila. Evolution, 10, 367-402.
Genotype data from Aleppo Pines
Description
Multiple sampled alleles from Aleppo Pine (Pinus halepensis) in the Eastern Mediterranean. Adapted from Gershberg et al. 2016.
Usage
genotypes
Source
Gershberg, A., Ne'eman, G., Ben-Shlomo, R. (2016). Genetic structure of a naturally regenerating post-fire seedling population: Pinus halepensis as a case study. Frontiers in Plant Science 7: 549.
Temporal allele frequency shifts
Description
Change in allele frequency over eight generations in the scarlet tiger moth (Callimorpha dominula).
Usage
moth
Source
Fisher, R. A. and E. B. Ford (1947). The Spread of a Gene in Natural Conditions in a Colony of the Moth Panaxia dominula. Heredity 1: 143-174.
SNP information for 25 loci
Description
Single Nucleotide Polymorphism data for 25 loci. Includes information on allele frequency, homozygosity, heterozygosity, chromosome location, and functional location of SNP.
Usage
snp
Source
1,000 Genomes Project (http://www.internationalgenome.org)
Genotypes across 13 CODIS loci
Description
Genotypes of 1,036 individuals across 13 core CODIS (Combined DNA Index System) loci, collected in the USA.
Usage
thirteen
Source
Hill, C.R., Duewer, D.L., Kline, M.C., Coble, M.D., and Butler, J.M. (2013) U.S. population data for 29 autosomal STR loci. Forensic Sci. Int. Genet. 7: e82-e83. Accessed from: https://strbase.nist.gov/fbicore.htm
Genotypes of 246 South Pacific Blue Whales
Description
Data frame of genotypes collected from 264 individual blue Whales (Balaenoptera musculus) across seven distinct loci. Adapted from Attard et al. 2012.
Usage
whale
Source
Attard, C. R., Beheregaray, L. B., Jenner, K. C. S., Gill, P. C., Jenner, M. N., Morrice, M. G., Robertson, K.M. and Moller, L. M. (2012). Hybridization of Southern Hemisphere blue whale subspecies and a sympatric area off Antarctica: impacts of whaling or climate change? Molecular Ecology, 21(23), 5715-5727.