bigmemoryExtras-package: An extension of the bigmemory package with added safety,...

In bigmemoryExtras: 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

bigmemoryExtras documentation built on Nov. 8, 2020, 5:17 p.m.