getG_symDMatrix {BGData}  R Documentation 
Computes a positive semidefinite symmetric genomic relation matrix G=XX'
offering options for centering and scaling the columns of X
beforehand.
getG_symDMatrix(X, center = TRUE, scale = TRUE, impute = TRUE, scaleG = TRUE,
minVar = 1e05, blockSize = 5000L,
folderOut = paste0("symDMatrix_", randomString()), vmode = "double",
i = seq_len(nrow(X)), j = seq_len(ncol(X)), chunkSize = 5000L,
nCores = getOption("mc.cores", 2L), verbose = FALSE)
X 
A matrixlike object, typically the genotypes of a 
center 
Either a logical value or a numeric vector of length equal to the
number of columns of 
scale 
Either a logical value or a numeric vector of length equal to the
number of columns of 
impute 
Indicates whether missing values should be imputed. Defaults to

scaleG 
TRUE/FALSE whether xx' must be scaled. 
minVar 
Columns with variance lower than this value will not be used in the
computation (only if 
blockSize 
The number of rows and columns of each block. If 
folderOut 
The path to the folder where to save the 
vmode 
vmode of 
i 
Indicates which rows of 
j 
Indicates which columns of 
chunkSize 
The number of columns of 
nCores 
The number of cores (passed to 
verbose 
Whether progress updates will be posted. Defaults to 
Even very large genomic relationship matrices are supported by partitioning
X
into blocks and calling getG
on these blocks. This function
performs the block computations sequentially, which may be slow. In an HPC
environment, performance can be improved by manually distributing these
operations to different nodes.
A symDMatrix
object.
multilevelparallelism
for more information on multilevel
parallelism. symDMatrixclass
and
BGDataclass
for more information on the BGData
class.
getG
to learn more about the underlying method.