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### =========================================================================
### TENxMatrix objects
### -------------------------------------------------------------------------
###
### Note that we could just wrap a TENxMatrixSeed object in a DelayedMatrix
### object to represent and manipulate a 10x Genomics dataset as a
### DelayedMatrix object. So, strictly speaking, we don't really need the
### TENxMatrix class. However, we define this class mostly for cosmetic
### reasons, that is, to hide the DelayedMatrix class from the user.
### So the user will see and manipulate TENxMatrix objects instead of
### DelayedMatrix objects.
###
setClass("TENxMatrix",
contains="DelayedMatrix",
representation(seed="TENxMatrixSeed")
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Constructor
###
setMethod("DelayedArray", "TENxMatrixSeed",
function(seed) new_DelayedArray(seed, Class="TENxMatrix")
)
### Works directly on a TENxMatrixSeed object, in which case it must be
### called with a single argument.
TENxMatrix <- function(filepath, group="matrix")
{
if (is(filepath, "TENxMatrixSeed")) {
if (!missing(group))
stop(wmsg("TENxMatrix() must be called with a single argument ",
"when passed a TENxMatrixSeed object"))
seed <- filepath
} else {
seed <- TENxMatrixSeed(filepath, group)
}
DelayedArray(seed)
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Taking advantage of sparsity
###
setMethod("nzcount", "TENxMatrix", function(x) nzcount(x@seed))
setMethod("read_sparse_block", "TENxMatrix",
function(x, viewport) read_sparse_block(x@seed, viewport)
)
setMethod("extractNonzeroDataByCol", "TENxMatrix",
function(x, j) extractNonzeroDataByCol(x@seed, j)
)
|
