Description Usage Arguments Details Value Note Examples
A set of wrapper functions for multicore processing, using the
parallel
package.
1 2 3 4 5 6 7 8 9 10  multicore.setup(max.cores = NULL)
multicore.currentCoreCount()
multicore.totalCoreCount()
multicore.samplePairs(sampleSet, symmetric.pairs = FALSE)
multicore.tapply(x, INDEX, FUN, ...)
multicore.lapply(x, FUN, ...)
multicore.by(data, INDICES, FUN, ...)

max.cores 
integer specifying how many cores to request. 
sampleSet 
character vector (or list of character vectors), usually SampleIDs, that
need to be turned into a list of all pairs from 
symmetric.pairs 
logical, are symmetric pairs needed. This is for cases where the function to be
called is sensitive to the order of its 2 arguments (i.e.

x, INDEX, FUN, ... 
the usual arguments passed on to the respective 'apply' function 
data, INDICES, FUN, ... 
the usual arguments passed on to the 'by' function 
These are simple wrappers around the parallel
routines, to facilitate
parcelling computations that involve entire chromosomes or samples out to
separate cores.
For multicore.setup
, the maximum of the number of cores actually available
or the number of cores requested. The function
tries to load package parallel
, and if successful, sets the number of
cores to be used. This value can be subsequently returned by multicore.currentCoreCount
.
For multicore.currentCoreCount
, integer telling the number of cores currently
requested via multicore.setup
.
For multicore.totalCoreCount
, integer telling the number of cores actually
present on this compute node. If multicore.setup
has not yet been called, it
does so and requests all cores available.
For multicore.samplePairs
, a list of vectors (each of length 2), suitable for
a call to multicore.lapply
for a function expecting a vector of length 2 as its
argument.
For multicore.tapply
and multicore.lapply
, the same type result as their
primitive functions, after being gathered from the separate cores.
All multicore functions turn off prescheduling ( mc.preschedule=FALSE
), because
we assume the processing time of each piece is highly variable.
All multicore functions turn off recursion ( mc.allow.recursive=FALSE
), because
we assume all available cores will be used by the parent call.
1  multicore.samplePairs( list( c("Tom", "Dick", "Harry"), c("Jack","Jill")), symmetric.pairs=TRUE)

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