mppData: Complete 'mppData' object

In mppR: Multi-Parent Population QTL Analysis

Complete mppData object

Description

Complete mppData object made from a sample data of the maize US nested association mapping (NAM) population. This mppData object went through all the steps of the data processing: create.mppData, QC.mppData, IBS.mppData, IBD.mppData, parent_cluster.mppData. The mppData contain all the data necessary for the QTL analysis procedures.

Usage

data(mppData)

Format

mppData

Details

The complete mppData object is a list containing the following elements:

1. geno.IBS: IBS genotype marker matrix.

2. geno.IBD: R/qtl cross.object containing the genotype within cross IBD probabilities.

3. geno.id: List of genotypes.

4. allele.ref: Matrix containing for each marker the most and least frequent marker scores and the two heterozygous scores.

5. geno.par: Parents marker matrix.

6. geno.par.clu: Parent marker data used to cluster the parents.

7. par.clu: Parent clustering results.

8. mono.anc: Positions for which the ancestral clustering was monomorphic.

9. pheno: Phenotypic trait matrix.

10. map: Genetic map corresponding to the geno (IBS, IBD, par) arguments.

11. haplo.map: Genetic map corresponding to geno.par.clu.

12. cross.ind: Vector indicating to which cross each genotype belongs.

13. par.per.cross: Matrix with for each cross the parent 1 and 2.

14. parents: Vector of parents.

15. type: Type of population.

16. n.cr: Number of crosses.

17. n.par: Number of parents.

18. n.anc: Average number of ancestral group along the genome.

19. n.zigo: Number of possible allelic computations 2 (AA/BB) or 3 (AA/AB/BB).

20. rem.mk: Removed markers in the data processing.

21. rem.gen: Removed genotypes in the data processing.

22. status: Indicates the level of progression in the data processing.

See Also

create.mppData, QC.mppData, IBS.mppData, IBD.mppData, parent_cluster.mppData

Examples

  data(mppData)

mppR documentation built on Jan. 6, 2023, 1:23 a.m.