NEWS.md

In BEDMatrix: Extract Genotypes from a PLINK .bed File

BEDMatrix 2.0.3

• Replace testthat with tinytest.
• Do not mix up minor/major and first/second alleles in documentation.

BEDMatrix 2.0.2

• Fix that BED files larger than 2GB cannot be loaded in Windows.
• Do not produce -Wunused-function warnings in exported BEDMatrix.h header.

BEDMatrix 2.0.1

• Fix extra ; outside of compute_num_bytes_per_variant function in exported BEDMatrix.h header (found by CRAN incoming checks).

BEDMatrix 2.0.0

• Extractions can be canceled with Control-c.
• Reimplement package in C, drop Rcpp.
• Genotypes can be extracted on the C level in other packages by adding BEDMatrix to the LinkingTo field of the DESCRIPTION file and including the BEDMatrix.h in your C code. The header file contains the BEDMatrix struct and the following functions: compute_num_bytes_per_variant(), extract_genotype_linear(), extract_genotype_cartesian(), and recode_genotype().

BEDMatrix 1.6.1

• Re-add C++11 requirement to avoid warnings from Boost headers on Windows.

BEDMatrix 1.6.0

• Follow Bioconductor S4 practices. If you have used new() to create BEDMatrix instances, please use the constructor BEDMatrix() instead.
• Fix non-character rownames or colnames when data.table package is installed.
• Drop C++11 requirement.
• Update citation instructions.

BEDMatrix 1.5.0

• Add simple_names option to BEDMatrix initialization function (contributed by Alex Ochoa).
• Fix single indexing for index values greater than .Machine$integer.max (previously generated NAs).
• Minor performance improvements.

BEDMatrix 1.4.1

• Specify fileset name in messages during instantiation.

BEDMatrix 1.4.0

• Support subsetting by NA.
• Use crochet package for subsetting
• Fix minor subsetting bugs
• Update example
• Remove intermediate S3 BEDMatrix type

BEDMatrix 1.3.0

• Speed up character subsetting.
• Speed up detection of n, p, rownames, and colnames during initialization if data.table package is installed.
• Support str function.

BEDMatrix 1.2.0

• Support path without extension (like PLINK).
• Add path attribute (to reattach instance after saving it to RData).
• Add length method.
• Add as.matrix method.
• Add is.matrix method.
• Store dimensions in S3 wrapper as dims attribute to allow for faster recreation when saved.
• Fix bug that modified i and j when subsetting.

BEDMatrix 1.1.0

• Restore cross-platform compatibility by dropping the system dependency on Boost.IOStreams in favor of Boost.Interprocess which provides header-only memory-mapping and is therefore supported by the BH package.

BEDMatrix 1.0.1

• Ensure that the same C compiler and compiler flags are used in the configure tests as when compiling R.
• Improve messages in configure script to distinguish between Boost headers and Boost libraries.

BEDMatrix 1.0.0

Initial release.

BEDMatrix documentation built on July 8, 2020, 7:26 p.m.