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changelog.md

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V0.2.0

  • Initial release

v0.2.1

  • Use a c++ function for counting lines instead of bash wc
  • Corrects bug in lassosum.pipeline() when calling some functions in data.table

v0.2.2

  • includes some additional objects in the output of validate.lassosum.pipeline() and pseudovalidate.lassosum.pipeline()
  • Allows the validate.function in validate.lassosum.pipeline() to be given as a character rather than a function.

v0.2.3

  • best.beta is output in validate.lassosum.pipeline() and pseudovalidate.lassosum.pipeline()
  • fixes bug when grouping blocks that are too small

v0.2.4

  • fixes bug when matching variable names in matchpos()
  • Support for parallel processing in the pgs() function, (and therefore validate.lassosum.pipeline() and pseudovalidate.lassosum.pipeline())
  • Allows summary statistics to be matched by SNP id as well as chromosome/position
  • fixes bug when the bfile is too large (due to integer overflow in c++)
  • adds a user-defined limit to the size of the bfile to discourage the use of large reference panels
  • cpp functions are now exported (except openPlinkBinaryFile())
  • includes this changelog file
  • fixes bug in plotting results from validate.lassosum.pipeline() and pseudovalidate.lassosum.pipeline()
  • fixes bug in displaying "Running lassosum with s=1..." message.
  • renames hg19 LD region files
  • adds hg38 LD region files (lifted over from the hg19 ones)

v0.2.5

  • Bug fix for lassosum.pipeline() in parsing LDblocks when given as a vector of factors
  • Bug fix for pgs() when extract is specified

v0.3.0

  • Adds function for cross-prediction link
  • Allows multiple bfiles in many functions

v0.3.1

  • Adds cp.meta() for meta-analysing external summary statistics with results from cp.plink.linear()
  • cp.plink.linear() will weight correlation by sample size when averaging across folds
  • A number of unrelated functions are now hidden.
  • Improved documentation for cp functions

v0.3.2

  • fixes bug in cp.plink.linear covar option
  • fixes bug when specifying keep
  • adds write.table2()

v0.4.0

  • Removes support for cross-prediction.
  • Cross-prediction moved to a separate package
  • recast validate.lassosum.pipeline(), pseudovalidate.lassosum.pipeline(), and pgs as S3 methods
  • Adds option for including covariates in validate.lassosum.pipelin()
  • bug fix in matchpos()
  • Introduces c++ function for pgs() with sparse matrix. Used as default.
  • p2cor() will automatically code to NA those correlations with relatively small n.
  • Always uses data.table::fread() for reading files

v0.4.1

  • Bug fix for matchpos()
  • pgs() stops if keep or extract not in the same order as in .bim/.fam file

v0.4.2

  • Allows covar and pheno to take data.frames or files as input.
  • You no longer have to re-enter test.bfile if keep or remove is used in validate.lassosum.pipeline() or pseudovalidate.lassosum.pipeline()
  • Adds splitvalidate() for split-validation.
  • Adds subset.lassosum.pipeline() for applying validated PGS to new data.
  • Allows pheno to be constant or NA if only one PGS is calculated in validate.lassosum.pipeline().
  • plot.validate.lassosum() will abandon if there are no finite values.
  • A standalone version of lassosum is available

v0.4.3

  • LDblocks does not need to be specified when s < 1
  • Better tracing in SD calculation
  • Bug fix in validate.lassosum.pipeline()
  • Allows multiple test.bfile in validate.lassosum.pipeline()

v0.4.4

  • Bug fix
  • Better documentation for Mac users

v0.4.5

  • [Bug fix] standalone version used to ignore --nthreads option when running validate.lassosum.pipeline
  • [Bug fix] The pheno and covar option didn't use to like data.table and required data.frame
  • [Bug fix] Pull request #20
  • Adds seed option in standalone version