G.matrix {ASRgenomics} | R Documentation |
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.
G.matrix(
M = NULL,
method = "VanRaden",
na.string = "NA",
sparseform = FALSE,
digits = 8,
message = TRUE
)
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 |
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).
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
).
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: 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"))