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NEWS.md

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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

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.