Quality control of the genomic file (ASRGenomics package in R)

Certainly! The ASRgenomics package in R provides a suite of molecular and genetic routines
to assist with analytical pipelines related to genomic data. It is particularly useful before and
after using ASReml-R or other libraries for tasks like Genomic Selection (GS) or Genome-
Wide Association Studies (GWAS)12.

Here are some key functionalities offered by ASRgenomics:

1. Filtering SNP Data for Quality Control: You can apply quality control filters to
SNP data to ensure data integrity.
2. Assessing Kinship Matrix (K): The package allows you to evaluate the kinship
matrix by reporting diagnostics (statistics and plots).
3. Principal Component Analysis (PCA): Perform PCA based on kinship or SNP
matrices to understand population structure.
4. Calculating Genomic Matrix (G): Calculate the genomic matrix G and assess its
quality.
5. Matching Pedigree-Based and Genomic-Based Matrices: Compare and align
pedigree-based matrices with genomic-based matrices.
6. Tuning Genomic Matrix: Adjust the genomic matrix (bend, blend, or align) as
needed.
7. Hybrid Matrix (H) Generation: Obtain the hybrid matrix H required for single-step
Genomic-BLUP (ssGBLUP)13.

For detailed usage instructions and examples, you can refer to the ASRgenomics User’s
Manual. The manual covers various aspects of data preparation, matrix calculations, and
complementary genomic analyses1.

Remember that ASRgenomics complements existing tools and libraries, enhancing your
genomic research capabilities in R. If you have specific tasks related to genomic quality
control, this package can be a valuable addition to your workflow.

Kinship matrix for accessions (Genomic relationship matrix GRM) (ASRGenomics package in R)

The ASRGenomics package in R provides a suite of molecular and genetic tools to assist in
analytical pipelines related to genomic selection and genome-wide association analyses. One
of the key functionalities it offers is the computation of the genomic relationship matrix
(GRM), also known as the genomic numerator relationship matrix.

Here are the details for the G.matrix function within the ASRGenomics package:

 Function Name: G.matrix

 Description: Generates the genomic numerator relationship matrix for additive
(VanRaden or Yang) or dominant (Su or Vitezica) relationships. The matrix provided,
denoted as boldsymbol {M}, has dimensions n times p, where n represents the
number of individuals and p denotes the number of markers. Individual and marker
names are assigned to row names and column names, respectively. SNP data is coded
as 0, 1, or 2 (integers or decimal numbers). If there are missing values, they need to be
specified.
 Method Options:
 o For additive matrix: “VanRaden” or “Yang”
o For dominant matrix: “Su” or “Vitezica”
 Output:
o If sparseform is set to FALSE, it provides the full genomic matrix
boldsymbol {G}.
o If sparseform is set to TRUE, it provides the genomic matrix in sparse form.
 References:
o Amadeu, R.R., Cellon, C., Olmstead, J.W., Garcia, A.A.F, Resende, M.F.R.,
and P.R. Munoz. 2016. AGHmatrix: R package to construct relationship
matrices for autotetraploid and diploid species: A blueberry example. The
Plant Genome 9 (3). doi: 10.3835/plantgenome2016.01.0009
 Example Usage:
 # Requesting a full matrix using VanRaden method
 # Get G matrix
 G <- G.matrix(M = geno.apple, method = "VanRaden")$G
 G[1:5, 1:5]

 # Requesting a sparse form using VanRaden method
 # Get G matrix
 G_sparse <- G.matrix(M = geno.apple, method = "VanRaden", sparseform
= TRUE)$G.sparse
 head(G_sparse)
 head(attr(G_sparse, "rowNames"))
 Package Documentation: ASRgenomics Package Documentation1

what is Kinship

Kinship is a fundamental concept in anthropology, encompassing the intricate web of social

relationships that shape human lives across all societies. Let’s delve into its meaning and
significance:

1. Definition:
o Kinship refers to the interconnectedness arising from biological and social
ties among individuals. These ties form the basis for cultural traditions,
societal norms, and personal identity.
o It encompasses both the patterns of social relationships themselves and the
study of these patterns in various human cultures.
2. Key Aspects:
o Basic Facts of Life: Anthropologist Robin Fox describes kinship as the study
of how humans navigate essential aspects of life, including mating, gestation,
parenthood, socialization, and siblingship.
o Social Ends: Kinship serves various social purposes, such as child
socialization and the formation of economic, political, and religious groups.
o Conceptualization: Unlike animals, humans can conceptualize and
categorize these raw materials of life to serve their social needs.
3. Terminology and Concepts:
o Descent: Refers to social relations during development.
o Marriage: Kinship extends to relationships formed through marriage, known
as affinity.
o Descent Group: The relationships within one’s group of origin.
o Fictive Kinship: Imagined or symbolic kinship ties.
 o Lineage: A group tracing descent from a common ancestor.
o Consanguinity: Blood-related kinship.
o Affine: Kinship through marriage.
o Totems: Some cultures consider descent groups to lead back to gods or animal
ancestors.
4. Biological Context:
o In biology, kinship often refers to genetic relatedness or the coefficient of
relationship between individuals within a species.
o This concept also applies to human relationships, where it aligns with
consanguinity or genealogy.
5. Family:
o Family encompasses people connected by consanguinity (birth), affinity
(marriage), or co-residence/shared consumption.
o It plays a crucial role in child socialization across most societies.

In summary, kinship weaves the intricate fabric of human connections, shaping our identities,
traditions, and social structures 123.