Description Usage Arguments Details Value Author(s) See Also
makeSparseMatrix
is used to create a sparse block-diagonal matrix from a dense matrix or a table of pairwise values, using a user-specified threshold for sparsity. An object of class Matrix
will be returned. A sparse matrix may be useful for fitting the association test null model with fitNullModel
when working with very large sample sizes.
1 2 3 4 5 6 7 8 9 10 11 12 | ## S4 method for signature 'data.table'
makeSparseMatrix(x, thresh = NULL, sample.include = NULL, diag.value = NULL,
verbose = TRUE)
## S4 method for signature 'data.frame'
makeSparseMatrix(x, thresh = NULL, sample.include = NULL, diag.value = NULL,
verbose = TRUE)
## S4 method for signature 'matrix'
makeSparseMatrix(x, thresh = 2^(-11/2), sample.include = NULL, diag.value = NULL,
verbose = TRUE)
## S4 method for signature 'Matrix'
makeSparseMatrix(x, thresh = 2^(-11/2), sample.include = NULL, diag.value = NULL,
verbose = TRUE)
|
x |
An object to coerce to a sparse matrix. May be of class |
thresh |
Value threshold for clustering samples to make the output matrix sparse block-diagonal. When |
sample.include |
An optional vector of sample.id indicating all samples that should be included in the output matrix; see 'Details' for usage. |
diag.value |
When |
verbose |
A logical indicating whether or not to print status updates to the console; the default is TRUE. |
sample.include
has two primary functions: 1) It can be used to subset samples provided in x
. 2) sample.include
can include sample.id not in x
; these additional samples will be included in the output matrix, with a value of 0 for all off-diagonal elements, and the value provided by diag.value
for the diagonal elements. When left NULL
, the function will determine the list of samples from what is observed in x
.
thresh
sets a threhsold for clustering samples such that any pair with a value greater than thresh
is in the same cluster. All values within a cluster are kept, even if they are below thresh
. All values between clusters are set to 0, creating a sparse, block-diagonal matrix. When thresh
is NULL
, no clustering is done and all samples are returned in one block. This feature is useful when converting a data.frame of kinship estimates to a matrix.
An object of class 'Matrix
'. Samples may be in a different order than in the input x
, as samples are sorted by ID or rowname within each block (including within the block of unrelateds).
Matthew P. Conomos
kingToMatrix
and pcrelateToMatrix
for functions that use this function.
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