Demerelate (version 0.9-2)

Example.Data: Example dataset for package Demerelate to calculate inter individual pairwise genetic relatedness.

Description

The dataset gives randomized loci information of populations with differently related individuals. Pop-FS-HS consists of 10 full siblings (45 pairs) combined of 10 half siblings (45 pairs). Pop-FS-Non consists of 10 full sibilings (45 pairs) and 10 random individuals (45 pairs). Pop-Non is a population of 20 random drawn individuals (180 pairs). Datasets are based on information of 8 diploid loci with total number in alleles indicated by column names, i.e. number of alleles = 5, 10, 15, 20, 25, 30, 35, 40. The dataset demerelref gives randomized loci information of a population with 1000 individuals. Dataset is based on information of 8 diploid loci with total number in alleles indicated by column names, i.e. number of alleles = 5, 10, 15, 20, 25, 30, 35, 40. The dataset demereldist gives randomized relative positions for each individual in the dataset.

Usage

data(demerelpop) data(demerelref) data(demereldist)

Details

Standard inputformat is given for all applications in a similar way. Table is formatted as dataframe with headers set as TRUE. Headernames are not necessary but recommended. First column contains sample IDs (mode=character), which must be unique. However, no proofreading is implemented yet, but double named individuals may lead to errors or strange results. Column two contains population information (mode=factor). Pairwise relatedness is only calculated within populations. If you want to compare pairwise individual comparisons of several populations you need to build a new fictive population. You should do that with caution, since hidden population structures may produce strange results. Column three and four containing two alleles of a diploid marker for the sample defined in column one. Each marker should be appended in pairwise columns from then on. Allele size should be sorted in columns with the small allele in the odd numbered column and the bigger in even numbered column for convenience. However, Demerelate will take care of not sorted allele sizes and handle it correctly. The same inputformat is used for reference populations. All populations of inputdata are used as reference if no reference is defined by reference.pop. Additionally, the distance data are given (tab.dist) by the same inputformat. In column three and four you will need to define the x and y coordinate of each individual either by relative x-y coordinates or by decimal degrees of geographic coordinates.

Example input. Every dataframe in Demerelate should be organized in this way.

Sample-ID	Population	locus.1.a	locus.1.b	locus.2.a	locus.2.b
...	Ind.Norway.01	Norway	001	002	001
002	...	Ind.Norway.02	Norway	001	003
002	005	...	Ind.Norway.03	Norway	001
004	003	004	...	Ind.Norway.04	Norway
002	005	006	008	...	Ind.Germany.01
Germany	001	001	001	006	...
Ind.Germany.02	Germany	002	002	001	007
...	Ind.Germany.03	Germany	001	006	001
004	...	Ind.Germany.04	Germany	003	004
001	002	...	Sample-ID	Population	locus.1.a

See Also

Demerelate Emp.calc Loci.test

Examples

# Please consult examples from Demerelate