bigmemoryExtras-package: An extension of the bigmemory package with added safety, convenience, and a factor class.
Description
This package defines a "BigMatrix" ReferenceClass which
adds safety and convenience features to the
filebacked.big.matrix class from the bigmemory package.
BigMatrix protects against segfaults by monitoring, and
gracefully restoring, the connection to on-disk data. It
also protects against accidental data modification with a
filesystem-based permissions system. We provide
functionality for using BigMatrix-derived classes as
assayData matrices within the Biobase package's eSet
family of classes. BigMatrix provides some optimizations
related to attaching to, and indexing into, file-backed
matrices with dimnames. Additionally, the package
provides a "BigMatrixFactor" class, a file-backed matrix
with factor properties.
Details
BigMatrix stores the filesystem path to its on-disk data.
When a big.matrix object is saved, e.g. with "save" the
external pointer to the on-disk data becomes "nil". Any
access to this nil pointer causes a segfault. A BigMatrix
object will gracefully re-attach itself to its on-disk
components any time use of the "nil" pointer is
attempted.
See Also
BigMatrix-class BigMatrixFactor-class BigMatrix
BigMatrixFactor filebacked.big.matrix ReferenceClasses