BGData 2.2.0

• Follow Bioconductor S4 practices.
  • If you have used new() to create BGData instances, please use the BGData() constructor function instead.
  • If you have used @ to access the slots of BGData instances, please use the geno(), pheno(), and map() accessors instead.
• BGData():
  • Do not create dimnames for geno as this object is likely shared.
  • Check if geno has row names before creating pheno stub.
  • Check if geno has column names before creating map stub.
  • Rename IID in pheno stub to sample_id.
  • Rename mrk in map stub to variant_id.
  • Change format of rownames for pheno stub to a sequence starting with sample_ and rownames for map stub to a sequence starting with variant_ if geno does not have dimnames.
• as.BGData():
  • Force column classes when loading .fam and .bim files.
  • Force FID and IID columns to be of type character when loading alternate phenotype files.
  • Do not make assumptions about the structure of dimnames of a BEDMatrix object if it is passed without .fam and .bim file unless they are NULL.
• Add validity tests for BGData objects:
  • Check if number of rows of geno matches number of rows of pheno.
  • Check if number of columns of geno matches number of rows of map.
  • Warn if the row names of pheno do not match the row names of geno.
  • Warn if the row names of map do not match the column names of geno.
• Add preprocess() function for fast centering, scaling, and imputation.
• GWAS(): Return number of records used for each variant and allele frequencies in rayOLS.
• Update citation instructions.
• Use inherits(., *) instead of class(.) == * (R4 compat).

BGData 2.1.0

• Add chunkedMap() function.
• Improve error handling in chunkedMap() and chunkedApply().
• summarize(): Improve performance.
• GWAS(): Improve performance of rayOLS method.
• GWAS(): Fix bug when computing p-values for methods other than rayOLS, lsfit, or SKAT when i is used to subset samples.
• GWAS(): Fix wrong results in lsfit method when covariates with missing values are used.
• as.BGData(): Fix bug loading .fam and .bim files when path contains the word bed.

BGData 2.0.0

Breaking Changes

• Rename bufferSize to chunkSize.
• Remove nTasks parameter from chunkedApply() and methods based on it.
• Remove crossprods function.

Other Changes

• Change chunking strategy to improve parallelism: instead of loading a subset of chunkSize in the main process, load a subset of chunkSize in the each fork. That way nTasks is not necessary anymore and the same code can be used for one core and multiple cores.
• Add findRelated() function for use with matrices and symDMatrix objects.
• Add orderedMerge() function that allows for phenotypes to be easily merged into a BGData object.
• Performance improvements in getG() function: use single shared memory matrix to collect results.
• Performance improvements in rayOLS method in GWAS() function.
• getG_symDMatrix(): Support version 2 of symDMatrix package.
• getG_symDMatrix(): Add chunkSize parameter.
• getG_symDMatrix(): Add minVar parameter.
• as.BGData(): Use rownames of BEDMatrix object as rownames for pheno, and colnames of BEDMatrix object as rownames for map.
• Include process ID in verbose output if nCores > 1.

Bug Fixes

• getG_symDMatrix(): Fix scaling error when scale = FALSE.
• getG_symDMatrix(): Compute block indices correctly for out-of-order, non-sequential indices.
• getG_symDMatrix(): Do not include centers and scales in attributes anymore because the influence of j and minVar is difficult to retain.

BGData 1.0.0

Initial release.