NEWS.md
In QuantGen/BGData: A Suite of Packages for Analysis of Big Genomic Data

BGData 2.4.1

Fixed minor native routine registration issue.
Drop defunct CI services.
Update link to paper.

BGData 2.4.0

Add FWD() function for performing forward regressions.

BGData 2.3.0

Add segments() function for finding non-overlapping segments based on a summary statistic.
preprocess(): Add nCores parameter.
findRelated(): Map indices to sample names for matrix inputs.
getG(): Add impute parameter.
getG(): Impute by mean instead of 0 if center = FALSE.
getG(): Use preprocess() internally for better performance.
as.BGData(): Read genetic distances in .bim file as double instead of integer.

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

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

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.

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.