G.matrix {ASRgenomics} | R Documentation |

## Obtains the genomic matrix from SNP data for additive or dominant relationships

### Description

Generates the genomic numerator relationship matrix for
additive (VanRaden or Yang) or dominant (Su or Vitezica) relationships.
Matrix provided `\boldsymbol{M}`

is of the form `n \times p`

, with `n`

individuals and `p`

markers.
Individual and
marker names are assigned to `rownames`

and `colnames`

, respectively.
SNP data is coded as 0, 1, 2 (integers or decimal numbers).
Missing values, if present, need to be specified.

### Usage

```
G.matrix(
M = NULL,
method = "VanRaden",
na.string = "NA",
sparseform = FALSE,
digits = 8,
message = TRUE
)
```

### Arguments

`M` |
A matrix with SNP data of form |

`method` |
The method considered for calculation of genomic matrix.
Options are: |

`na.string` |
A character that is interpreted as missing values (default = |

`sparseform` |
If |

`digits` |
Set up the number of digits used to round the output matrix (default = 8). |

`message` |
If |

### Details

Note: If data is provided with missing values, it will process calculations of relationships on pairwise non-missing data.

It uses function `Gmatrix`

for calculations
from R package AGHmatrix (Amadeu *et al.* 2019).

### Value

A list with one of these two elements:

`G`

: the`\boldsymbol{G}`

matrix in full form (only if`sparseform = FALSE`

).`G.sparse`

: the`\boldsymbol{G}`

matrix in sparse form (only if`sparseform = TRUE`

).

### References

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

### Examples

```
# Example: Requesting a full matrix by VanRanden.
# Get G matrix.
G <- G.matrix(M = geno.apple, method = "VanRaden")$G
G[1:5, 1:5]
# Example: Requesting a sparse form by VanRanden.
# Get G matrix.
G <- G.matrix(M = geno.apple, method = "VanRaden", sparseform = TRUE)$G.sparse
head(G)
head(attr(G, "rowNames"))
```

*ASRgenomics*version 1.1.4 Index]