chunkedMap()
function.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
.bufferSize
to chunkSize
.nTasks
parameter from chunkedApply()
and methods based on it.crossprods
function.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.findRelated()
function for use with matrices and symDMatrix objects.orderedMerge()
function that allows for phenotypes to be easily merged into a BGData object.getG()
function: use single shared memory matrix to collect results.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.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.Initial release.