- individualData
Individual data from which the consensus is to be calculated. It can be either a list or a
multiData
structure. Each element in individulData
can in turn either be a numeric
object (vector, matrix or array) or a BlockwiseData
structure.
- consensusTree
A list specifying the consensus calculation. See details.
- level
Integer which the user should leave at 1. This serves to keep default set names unique.
- useBlocks
When individualData
contains BlockwiseData
, this argument can be an
integer vector with indices of blocks for which the calculation should be performed.
- randomSeed
If non-NULL
, the function will save the current state of the random generator, set the given seed,
and restore the random seed to its original state upon exit. If NULL
, the seed is not set nor is it
restored on exit.
- saveCalibratedIndividualData
Logical: should calibrated individual data be saved?
- calibratedIndividualDataFilePattern
Pattern from which file names for saving calibrated individual data are determined. The conversions
%a
, %s
and %b
will be replaced by analysis name, set number and block number,
respectively.
- saveConsensusData
Logical: should final consensus be saved (TRUE
) or returned in the return value (FALSE
)?
- consensusDataFileNames
Pattern from which file names for saving the final consensus are determined. The conversions
%a
and %b
will be replaced by analysis name and block number,
respectively.
- getCalibrationSamples
When calibration method in the consensusOptions
component of ConsensusTree
is "single
quantile"
, this logical argument determines whether the calibration samples should be returned within the
return value.
- keepIntermediateResults
Logical: should results of intermediate consensus calculations (if any) be kept? These are always returned
as BlockwiseData
whose data are saved to disk.
- useDiskCache
Logical: should disk cache be used for consensus calculations? The disk cache can be used to store chunks of
calibrated data that are small enough to fit one chunk from each set into memory (blocks may be small enough
to fit one block of one set into memory, but not small enough to fit one block from all sets in a consensus
calculation into memory at the same time). Using disk cache is slower but lessens the memory footprint of
the calculation.
As a general guide, if individual data are split into blocks, we
recommend setting this argument to TRUE
. If this argument is NULL
, the function will decide
whether to use disk cache based on the number of sets and block sizes.
- chunkSize
Integer giving the chunk size. If left NULL
, a suitable size will be chosen automatically.
- cacheDir
Directory in which to save cache files. The files are deleted on normal exit but persist if the function
terminates abnormally.
- cacheBase
Base for the file names of cache files.
- collectGarbage
Logical: should garbage collection be forced after each major calculation?
- verbose
Integer level of verbosity of diagnostic messages. Zero means silent, higher values make the output
progressively more and more verbose.
- indent
Indentation for diagnostic messages. Zero means no indentation, each unit adds
two spaces.